data_6T6I

_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  6T6I
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    6T6I
_pdbx_vrpt_summary.PDB_deposition_date         2019-10-18
_pdbx_vrpt_summary.PDB_revision_number         4
_pdbx_vrpt_summary.PDB_revision_date           2024-01-24
_pdbx_vrpt_summary.report_creation_date        2024-06-24:11:41
_pdbx_vrpt_summary.attempted_validation_steps  molprobity,validation-pack,xtriage,eds,mogul,percentiles,writexml,writecif,writepdf
_pdbx_vrpt_summary.ligands_for_buster_report   N
#
loop_
_pdbx_vrpt_entity.id
_pdbx_vrpt_entity.type
_pdbx_vrpt_entity.description
1  polymer      "Pol protein"  
2  non-polymer  "NICKEL (II) ION"  
3  water        water  
#
loop_
_pdbx_vrpt_asym.label_asym_id
_pdbx_vrpt_asym.entity_id
A  1  
B  2  
C  3  
#
loop_
_pdbx_vrpt_percentile_list.id
_pdbx_vrpt_percentile_list.range
_pdbx_vrpt_percentile_list.exp_method
1  all    x-ray  
2  2.203  x-ray  
#
loop_
_pdbx_vrpt_percentile_type.id
_pdbx_vrpt_percentile_type.type
1  all_atom_clashscore           
2  Ramachandran_outlier_percent  
3  rotamer_outliers_percent      
4  RSRZ_outliers_percent         
5  R_value_R_free                
#
loop_
_pdbx_vrpt_percentile_conditions.id
_pdbx_vrpt_percentile_conditions.percentile_list_id
_pdbx_vrpt_percentile_conditions.type_id
_pdbx_vrpt_percentile_conditions.rank
_pdbx_vrpt_percentile_conditions.number_entries_total
_pdbx_vrpt_percentile_conditions.res_high
_pdbx_vrpt_percentile_conditions.res_low
 1  1  1   95.53  141614     ?     ?  
 2  2  1   97.19    5594  2.20  2.20  
 3  1  2  100.00  138981     ?     ?  
 4  2  2  100.00    5503  2.20  2.20  
 5  1  3  100.00  138945     ?     ?  
 6  2  3  100.00    5504  2.20  2.20  
 7  1  4    9.29  127900     ?     ?  
 8  2  4    8.00    4800  2.20  2.20  
 9  1  5   57.97  130704     ?     ?  
10  2  5   72.68    4898  2.20  2.20  
#
loop_
_pdbx_vrpt_percentile_entity_view.ordinal
_pdbx_vrpt_percentile_entity_view.conditions_id
_pdbx_vrpt_percentile_entity_view.type_id
_pdbx_vrpt_percentile_entity_view.label_asym_id
_pdbx_vrpt_percentile_entity_view.PDB_model_num
_pdbx_vrpt_percentile_entity_view.entity_id
_pdbx_vrpt_percentile_entity_view.auth_asym_id
_pdbx_vrpt_percentile_entity_view.rank
1  3  2  A  1  1  A  100.00  
2  4  2  A  1  1  A  100.00  
3  5  3  A  1  1  A  100.00  
4  6  3  A  1  1  A  100.00  
5  7  4  A  1  1  A    9.29  
6  8  4  A  1  1  A    8.00  
#
_pdbx_vrpt_summary_entity_geometry.ordinal          1
_pdbx_vrpt_summary_entity_geometry.PDB_model_num    1
_pdbx_vrpt_summary_entity_geometry.entity_id        1
_pdbx_vrpt_summary_entity_geometry.label_asym_id    A
_pdbx_vrpt_summary_entity_geometry.auth_asym_id     A
_pdbx_vrpt_summary_entity_geometry.angles_RMSZ      0.41
_pdbx_vrpt_summary_entity_geometry.bonds_RMSZ       0.24
_pdbx_vrpt_summary_entity_geometry.num_bonds_RMSZ   489
_pdbx_vrpt_summary_entity_geometry.num_angles_RMSZ  659
#
_pdbx_vrpt_summary_geometry.ordinal                        1
_pdbx_vrpt_summary_geometry.percent_ramachandran_outliers  0.00
_pdbx_vrpt_summary_geometry.percent_rotamer_outliers       0.00
_pdbx_vrpt_summary_geometry.clashscore                     1.05
_pdbx_vrpt_summary_geometry.num_H_reduce                   479
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ                 489
_pdbx_vrpt_summary_geometry.bonds_RMSZ                     0.24
_pdbx_vrpt_summary_geometry.num_angles_RMSZ                659
_pdbx_vrpt_summary_geometry.angles_RMSZ                    0.41
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            30.223
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         45.342
_pdbx_vrpt_summary_diffraction.I_over_sigma              8.05(2.20A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        3043
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.393
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.461
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.286
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.947
_pdbx_vrpt_summary_diffraction.twin_fraction             h,-h-k,-l:0.168
_pdbx_vrpt_summary_diffraction.DCC_R                     0.23
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.23
_pdbx_vrpt_summary_diffraction.EDS_R                     0.23
_pdbx_vrpt_summary_diffraction.EDS_res_high              2.20
_pdbx_vrpt_summary_diffraction.EDS_res_low               42.89
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[35.874,35.874,85.372,0.000,0.000,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.945
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The largest off-origin peak in the Patterson function is 10.32% of the height of the origin peak. No significant pseudotranslation is detected."
_pdbx_vrpt_summary_diffraction.B_factor_type             FULL
_pdbx_vrpt_summary_diffraction.acentric_outliers         2
_pdbx_vrpt_summary_diffraction.centric_outliers          0
_pdbx_vrpt_summary_diffraction.data_completeness         99.97
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      335
_pdbx_vrpt_summary_diffraction.percent_free_reflections  11.01
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     8.93
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       2.20
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        42.89
_pdbx_vrpt_summary_diffraction.PDB_R                     0.22
_pdbx_vrpt_summary_diffraction.PDB_Rfree                 0.26
#
loop_
_pdbx_vrpt_model_instance.id
_pdbx_vrpt_model_instance.PDB_model_num
_pdbx_vrpt_model_instance.entity_id
_pdbx_vrpt_model_instance.label_asym_id
_pdbx_vrpt_model_instance.label_seq_id
_pdbx_vrpt_model_instance.label_comp_id
_pdbx_vrpt_model_instance.auth_asym_id
_pdbx_vrpt_model_instance.auth_seq_id
_pdbx_vrpt_model_instance.label_alt_id
_pdbx_vrpt_model_instance.PDB_ins_code
_pdbx_vrpt_model_instance.count_clashes
 1  1  1  A   4  HIS  A  215  .  ?        ?  
 2  1  1  A   5  HIS  A  216  .  ?        ?  
 3  1  1  A   6  HIS  A  217  .  ?        ?  
 4  1  1  A   7  HIS  A  218  .  ?        ?  
 5  1  1  A   8  HIS  A  219  .  ?        ?  
 6  1  1  A   9  ILE  A  220  .  ?        ?  
 7  1  1  A  10  GLN  A  221  .  ?        ?  
 8  1  1  A  11  ASN  A  222  .  ?        ?  
 9  1  1  A  12  PHE  A  223  .  ?        ?  
10  1  1  A  13  ARG  A  224  .  ?        ?  
11  1  1  A  14  VAL  A  225  .  ?        ?  
12  1  1  A  15  TYR  A  226  .  ?        ?  
13  1  1  A  16  TYR  A  227  .  ?        ?  
14  1  1  A  17  ARG  A  228  .  ?        ?  
15  1  1  A  18  ASP  A  229  .  ?        ?  
16  1  1  A  19  SER  A  230  .  ?        ?  
17  1  1  A  20  ARG  A  231  .  ?        ?  
18  1  1  A  21  ASP  A  232  .  ?        ?  
19  1  1  A  22  PRO  A  233  .  ?        ?  
20  1  1  A  23  ILE  A  234  .  ?        ?  
21  1  1  A  24  TRP  A  235  .  ?        ?  
22  1  1  A  25  LYS  A  236  .  ?        ?  
23  1  1  A  26  GLY  A  237  .  ?        ?  
24  1  1  A  27  PRO  A  238  .  ?        ?  
25  1  1  A  28  ALA  A  239  .  ?        ?  
26  1  1  A  29  LYS  A  240  .  ?        ?  
27  1  1  A  30  LEU  A  241  .  ?        ?  
28  1  1  A  31  LEU  A  242  .  ?        ?  
29  1  1  A  32  TRP  A  243  .  ?        ?  
30  1  1  A  33  LYS  A  244  .  ?        ?  
31  1  1  A  34  GLY  A  245  .  ?        ?  
32  1  1  A  35  GLU  A  246  .  ?        ?  
33  1  1  A  36  GLY  A  247  .  ?        ?  
34  1  1  A  37  ALA  A  248  .  ?        ?  
35  1  1  A  38  VAL  A  249  .  ?        ?  
36  1  1  A  39  VAL  A  250  .  ?        ?  
37  1  1  A  40  ILE  A  251  .  ?        2  
38  1  1  A  41  GLN  A  252  .  ?        ?  
39  1  1  A  42  ASP  A  253  .  ?        ?  
40  1  1  A  43  ASN  A  254  .  ?        ?  
41  1  1  A  44  SER  A  255  .  ?        ?  
42  1  1  A  45  ASP  A  256  .  ?        ?  
43  1  1  A  46  ILE  A  257  .  ?        ?  
44  1  1  A  47  LYS  A  258  .  ?        ?  
45  1  1  A  48  VAL  A  259  .  ?        ?  
46  1  1  A  49  VAL  A  260  .  ?        ?  
47  1  1  A  50  PRO  A  261  .  ?        ?  
48  1  1  A  51  ARG  A  262  .  ?        ?  
49  1  1  A  52  ARG  A  263  .  ?        ?  
50  1  1  A  53  LYS  A  264  .  ?        ?  
51  1  1  A  54  ALA  A  265  .  ?        ?  
52  1  1  A  55  LYS  A  266  .  ?        ?  
53  1  1  A  56  ILE  A  267  .  ?        ?  
54  1  1  A  57  ILE  A  268  .  ?        ?  
55  1  1  A  58  ARG  A  269  .  ?        ?  
56  1  1  A  59  ASP  A  270  .  ?        ?  
57  1  2  B   .  NI   A  301  .  ?        ?  
58  1  3  C   .  HOH  A  401  .  ?        ?  
59  1  3  C   .  HOH  A  402  .  ?        ?  
60  1  3  C   .  HOH  A  403  .  ?        ?  
61  1  3  C   .  HOH  A  404  .  ?        ?  
#
loop_
_pdbx_vrpt_model_instance_geometry.ordinal
_pdbx_vrpt_model_instance_geometry.instance_id
_pdbx_vrpt_model_instance_geometry.rotamer_class
_pdbx_vrpt_model_instance_geometry.phi
_pdbx_vrpt_model_instance_geometry.psi
_pdbx_vrpt_model_instance_geometry.ramachandran_class
_pdbx_vrpt_model_instance_geometry.cis_peptide
_pdbx_vrpt_model_instance_geometry.num_H_reduce
_pdbx_vrpt_model_instance_geometry.OWAB
_pdbx_vrpt_model_instance_geometry.num_bonds_RMSZ
_pdbx_vrpt_model_instance_geometry.bonds_RMSZ
_pdbx_vrpt_model_instance_geometry.num_angles_RMSZ
_pdbx_vrpt_model_instance_geometry.angles_RMSZ
_pdbx_vrpt_model_instance_geometry.program_for_bond_angle_geometry
_pdbx_vrpt_model_instance_geometry.average_occupancy
 1   1  t60           ?       ?  ?        ?        6  66.590    11  0.16    15  0.19  molprobity  1.000  
 2   2  t-80     -155.3   143.5  Favored  ?        7  58.160    11  0.14    15  0.35  molprobity  1.000  
 3   3  m-70     -102.0   100.3  Favored  ?        7  51.260    11  0.23    15  0.34  molprobity  1.000  
 4   4  m80       -69.6   128.9  Favored  ?        7  51.460    11  0.19    15  0.26  molprobity  1.000  
 5   5  p80       -78.0   155.5  Favored  ?        7  53.940    11  0.20    15  0.38  molprobity  1.000  
 6   6  mt        -65.8   123.1  Favored  ?       11  55.540     8  0.26    11  0.42  molprobity  1.000  
 7   7  mm-40     -66.0   142.2  Favored  ?        8  63.710     9  0.22    12  0.35  molprobity  1.000  
 8   8  m-20       65.4    47.9  Favored  ?        6  63.980     8  0.17    11  0.40  molprobity  1.000  
 9   9  m-85     -154.7   120.2  Favored  ?        9  59.590    12  0.41    16  0.36  molprobity  1.000  
10  10  mpt_?    -125.2   144.1  Favored  ?       13  63.910    11  0.20    14  0.40  molprobity  1.000  
11  11  t        -125.9   138.9  Favored  ?        9  52.300     7  0.20    10  0.43  molprobity  1.000  
12  12  m-85     -111.0   132.4  Favored  ?        9  55.680    13  0.24    18  0.34  molprobity  1.000  
13  13  p90      -131.3   151.5  Favored  ?        9  53.910    13  0.31    18  0.41  molprobity  1.000  
14  14  ttp180   -115.1   114.3  Favored  ?       13  74.310    11  0.21    14  0.46  molprobity  1.000  
15  15  m-20      -68.1   149.3  Favored  ?        4  76.350     8  0.17    11  0.36  molprobity  1.000  
16  16  t         -57.6   131.9  Favored  ?        5  86.900     6  0.18     8  0.36  molprobity  1.000  
17  17  mmp_?      72.9    33.1  Allowed  ?       13  93.020    11  0.21    14  0.40  molprobity  1.000  
18  18  t70      -154.7   115.6  Favored  ?        4  82.070     8  0.19    12  0.41  molprobity  1.000  
19  19  Cg_endo   -76.4   -10.7  Favored  ?        7  74.040     8  0.26    11  0.45  molprobity  1.000  
20  20  mt        -77.0   132.5  Favored  ?       11  73.010     8  0.21    11  0.33  molprobity  1.000  
21  21  m95       -83.1   140.6  Favored  ?       10  62.980    16  0.16    23  0.26  molprobity  1.000  
22  22  tptm     -114.6   153.7  Favored  ?       13  69.130     9  0.28    11  0.33  molprobity  1.000  
23  23  ?         142.4  -167.3  Favored  Y        3  61.920     4  0.48     6  0.62  molprobity  1.000  
24  24  Cg_endo   -73.7   145.2  Favored  ?        7  59.070     8  0.18    11  0.26  molprobity  1.000  
25  25  ?        -113.9   161.0  Favored  ?        5  50.500     5  0.35     7  0.50  molprobity  1.000  
26  26  mttt      -91.4   140.7  Favored  ?       13  57.460     9  0.26    11  0.29  molprobity  1.000  
27  27  tp        -87.9   124.8  Favored  ?       11  45.600     8  0.23    11  0.33  molprobity  1.000  
28  28  mt       -107.2   -27.6  Favored  ?       11  52.380     8  0.18    11  0.62  molprobity  1.000  
29  29  t-105    -160.5   151.7  Favored  ?       10  46.770    16  0.16    23  0.33  molprobity  1.000  
30  30  pttp     -133.7   113.5  Favored  ?       13  68.520     9  0.26    11  0.36  molprobity  1.000  
31  31  ?        -103.6  -162.0  Favored  ?        3  74.710     4  0.39     5  0.55  molprobity  1.000  
32  32  mm-40     -80.7   -41.8  Favored  ?        6  81.200     9  0.25    12  0.36  molprobity  1.000  
33  33  ?        -119.7    -7.3  Favored  ?        3  67.530     4  0.30     5  0.19  molprobity  1.000  
34  34  ?        -144.8   169.2  Favored  ?        5  58.110     5  0.35     7  0.65  molprobity  1.000  
35  35  m        -136.1   149.5  Favored  ?        9  52.490     7  0.19    10  0.49  molprobity  1.000  
36  36  t        -100.1   127.5  Favored  ?        9  45.990     7  0.24    10  0.42  molprobity  1.000  
37  37  pp       -126.8   159.1  Favored  ?       11  49.890     8  0.20    11  0.60  molprobity  1.000  
38  38  tt0      -124.5   108.5  Favored  ?        8  53.480     9  0.24    12  0.49  molprobity  1.000  
39  39  t70       -98.9    93.7  Favored  ?        4  65.120     8  0.21    11  0.58  molprobity  1.000  
40  40  t-20       65.0  -111.2  Allowed  ?        6  70.870     8  0.25    11  0.40  molprobity  1.000  
41  41  p        -101.7     8.6  Favored  ?        5  67.790     6  0.24     8  0.38  molprobity  1.000  
42  42  m-20     -112.3   124.5  Favored  ?        4  63.530     8  0.18    11  0.36  molprobity  1.000  
43  43  mt       -107.3   123.7  Favored  ?       11  51.240     8  0.23    11  0.50  molprobity  1.000  
44  44  mttt     -132.8   156.6  Favored  ?       13  55.680     9  0.26    11  0.51  molprobity  1.000  
45  45  t         -99.8   130.4  Favored  ?        9  45.240     7  0.20    10  0.44  molprobity  1.000  
46  46  t        -129.1   123.8  Favored  ?        9  48.130     7  0.21    11  0.46  molprobity  1.000  
47  47  Cg_exo    -57.7   144.6  Favored  ?        7  55.800     8  0.12    11  0.33  molprobity  1.000  
48  48  tpp85     -54.2   -34.7  Favored  ?       13  72.640    11  0.22    14  0.30  molprobity  1.000  
49  49  mtp-105   -62.7   -26.5  Favored  ?       13  72.530    11  0.24    14  0.56  molprobity  1.000  
50  50  mttm     -102.7    25.9  Favored  ?       13  67.120     9  0.25    11  0.28  molprobity  1.000  
51  51  ?        -134.8   146.1  Favored  ?        5  67.820     5  0.37     7  0.61  molprobity  1.000  
52  52  mtpp     -126.8    91.0  Favored  ?       13  74.740     9  0.32    11  0.54  molprobity  1.000  
53  53  pt        -79.7   134.4  Favored  ?       11  69.350     8  0.24    11  0.38  molprobity  1.000  
54  54  mt       -132.1   116.8  Favored  ?       11  67.010     8  0.26    11  0.42  molprobity  1.000  
55  55  mtt-85    -80.4   162.2  Favored  ?       13  75.210    11  0.22    14  0.55  molprobity  1.000  
56  56  m-20          ?       ?  ?        ?        4  80.480     7  0.13     8  0.25  molprobity  1.000  
57  57  ?             ?       ?  ?        ?        ?  84.690     ?     ?     ?     ?  ?           0.330  
58  58  ?             ?       ?  ?        ?        ?  63.600     ?     ?     ?     ?  ?           1.000  
59  59  ?             ?       ?  ?        ?        ?  57.780     ?     ?     ?     ?  ?           1.000  
60  60  ?             ?       ?  ?        ?        ?  48.510     ?     ?     ?     ?  ?           1.000  
61  61  ?             ?       ?  ?        ?        ?  64.030     ?     ?     ?     ?  ?           1.000  
#
loop_
_pdbx_vrpt_instance_clashes.ordinal
_pdbx_vrpt_instance_clashes.instance_id
_pdbx_vrpt_instance_clashes.label_atom_id
_pdbx_vrpt_instance_clashes.cid
_pdbx_vrpt_instance_clashes.clashmag
_pdbx_vrpt_instance_clashes.dist
1  37  C     1  0.44  2.38  
2  37  HD12  1  0.44  2.38  
#
loop_
_pdbx_vrpt_model_instance_density.ordinal
_pdbx_vrpt_model_instance_density.instance_id
_pdbx_vrpt_model_instance_density.natoms_eds
_pdbx_vrpt_model_instance_density.RSRCC
_pdbx_vrpt_model_instance_density.RSR
_pdbx_vrpt_model_instance_density.RSRZ
 1   1  10  0.856  0.189   0.849  
 2   2  10  0.908  0.121  -0.268  
 3   3  10  0.925  0.155   0.291  
 4   4  10  0.918  0.179   0.685  
 5   5  10  0.945  0.161   0.389  
 6   6   8  0.952  0.147   0.032  
 7   7   9  0.902  0.116  -0.595  
 8   8   8  0.851  0.168   0.390  
 9   9  11  0.913  0.153   0.315  
10  10  11  0.821  0.183   0.293  
11  11   7  0.966  0.138  -0.034  
12  12  12  0.919  0.141   0.156  
13  13  12  0.955  0.138   0.098  
14  14  11  0.755  0.247   1.213  
15  15   8  0.696  0.235   1.331  
16  16   6  0.317  0.287   2.516  
17  17  11  0.584  0.363   2.879  
18  18   8  0.901  0.206   0.899  
19  19   7  0.911  0.125  -0.095  
20  20   8  0.894  0.244   1.841  
21  21  14  0.891  0.157   0.575  
22  22   9  0.804  0.248   0.948  
23  23   4  0.812  0.144   0.244  
24  24   7  0.897  0.139   0.143  
25  25   5  0.962  0.117  -0.240  
26  26   9  0.943  0.162  -0.200  
27  27   8  0.955  0.136  -0.182  
28  28   8  0.959  0.178   0.591  
29  29  14  0.946  0.155   0.534  
30  30   9  0.843  0.230   0.708  
31  31   4  0.915  0.155   0.422  
32  32   9  0.901  0.330   2.115  
33  33   4  0.968  0.123  -0.095  
34  34   5  0.960  0.130  -0.009  
35  35   7  0.936  0.158   0.342  
36  36   7  0.965  0.156   0.305  
37  37   8  0.968  0.162   0.312  
38  38   9  0.932  0.110  -0.682  
39  39   8  0.930  0.164   0.272  
40  40   8  0.881  0.161   0.282  
41  41   6  0.955  0.133  -0.030  
42  42   8  0.932  0.112  -0.504  
43  43   8  0.930  0.122  -0.435  
44  44   9  0.907  0.196   0.254  
45  45   7  0.947  0.161   0.398  
46  46   7  0.963  0.189   0.925  
47  47   7  0.951  0.141   0.177  
48  48  11  0.855  0.189   0.379  
49  49  11  0.862  0.207   0.638  
50  50   9  0.975  0.137  -0.534  
51  51   5  0.946  0.162   0.560  
52  52   9  0.854  0.379   2.697  
53  53   8  0.895  0.234   1.655  
54  54   8  0.904  0.197   0.965  
55  55  11  0.819  0.156  -0.095  
56  56   8  0.758  0.302   2.331  
57  57   1  0.997  0.365       ?  
58  58   1  0.457  0.408       ?  
59  59   1  0.892  0.192       ?  
60  60   1  0.776  0.113       ?  
61  61   1  0.659  0.205       ?  
#
loop_
_pdbx_vrpt_software.ordinal
_pdbx_vrpt_software.name
_pdbx_vrpt_software.version
_pdbx_vrpt_software.success_y_or_n
1  molprobity   4.02b-467                                                             Y  
2  mogul        unknown                                                               Y  
3  eds          2.37.1                                                                Y  
4  dcc          '"2.27  (2023-04-10)"'                                                Y  
5  xtriage      1.20.1                                                                Y  
6  percentiles  "20191225.v01 (using entries in the PDB archive December 25th 2019)"  Y  
##
