data_8D05

_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  8D05
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    8D05
_pdbx_vrpt_summary.PDB_deposition_date         2022-05-25
_pdbx_vrpt_summary.PDB_revision_number         1
_pdbx_vrpt_summary.PDB_revision_date           2022-09-28
_pdbx_vrpt_summary.report_creation_date        2022-09-20:16:04
_pdbx_vrpt_summary.attempted_validation_steps  molprobity,validation-pack,xtriage,eds,percentiles,writexml,writecif,writepdf
_pdbx_vrpt_summary.ligands_for_buster_report   N
#
_pdbx_vrpt_entity.id           1
_pdbx_vrpt_entity.type         polymer
_pdbx_vrpt_entity.description  HALC2_065
#
_pdbx_vrpt_asym.label_asym_id  A
_pdbx_vrpt_asym.entity_id      1
#
loop_
_pdbx_vrpt_percentile_list.id
_pdbx_vrpt_percentile_list.range
_pdbx_vrpt_percentile_list.exp_method
1  all   x-ray  
2  2.51  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   54.55  141614     ?     ?  
 2  2  1   72.60    5346  2.50  2.50  
 3  1  2  100.00  138981     ?     ?  
 4  2  2  100.00    5231  2.50  2.50  
 5  1  3   56.63  138945     ?     ?  
 6  2  3   80.09    5233  2.50  2.50  
 7  1  4  100.00  127900     ?     ?  
 8  2  4  100.00    4559  2.50  2.50  
 9  1  5   27.11  130704     ?     ?  
10  2  5   46.19    4661  2.50  2.50  
#
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   56.63  
4  6  3  A  1  1  A   80.09  
5  7  4  A  1  1  A  100.00  
6  8  4  A  1  1  A  100.00  
#
_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      0.50
_pdbx_vrpt_summary_entity_geometry.bonds_RMSZ       0.24
_pdbx_vrpt_summary_entity_geometry.num_bonds_RMSZ   472
_pdbx_vrpt_summary_entity_geometry.num_angles_RMSZ  638
#
_pdbx_vrpt_summary_geometry.ordinal                        1
_pdbx_vrpt_summary_geometry.percent_ramachandran_outliers  0.00
_pdbx_vrpt_summary_geometry.percent_rotamer_outliers       1.89
_pdbx_vrpt_summary_geometry.clashscore                     5.18
_pdbx_vrpt_summary_geometry.num_H_reduce                   497
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ                 472
_pdbx_vrpt_summary_geometry.bonds_RMSZ                     0.24
_pdbx_vrpt_summary_geometry.num_angles_RMSZ                638
_pdbx_vrpt_summary_geometry.angles_RMSZ                    0.50
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.Babinet_b                 130.717
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            57.171
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         70.188
_pdbx_vrpt_summary_diffraction.I_over_sigma              1.06(2.51A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        2000
_pdbx_vrpt_summary_diffraction.Babinet_k                 0.239
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.305
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.518
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.351
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.938
_pdbx_vrpt_summary_diffraction.twin_fraction             h,-k,-l:0.075
_pdbx_vrpt_summary_diffraction.DCC_R                     0.24
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.26
_pdbx_vrpt_summary_diffraction.EDS_R                     0.25
_pdbx_vrpt_summary_diffraction.EDS_res_high              2.51
_pdbx_vrpt_summary_diffraction.EDS_res_low               50.19
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[74.042,74.042,61.993,0.000,0.000,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.172
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The largest off-origin peak in the Patterson function is 10.89% 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         0
_pdbx_vrpt_summary_diffraction.centric_outliers          0
_pdbx_vrpt_summary_diffraction.data_completeness         99.90
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      114
_pdbx_vrpt_summary_diffraction.percent_free_reflections  5.70
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     0.00
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       2.51
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        50.19
_pdbx_vrpt_summary_diffraction.PDB_R                     0.24
_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   9  PRO  A   9  .  ?        ?  
 2  1  1  A  10  ILE  A  10  .  ?        ?  
 3  1  1  A  11  VAL  A  11  .  ?        ?  
 4  1  1  A  12  ILE  A  12  .  ?        ?  
 5  1  1  A  13  ASP  A  13  .  ?        ?  
 6  1  1  A  14  LEU  A  14  .  ?        1  
 7  1  1  A  15  ASN  A  15  .  ?        ?  
 8  1  1  A  16  LYS  A  16  .  ?        ?  
 9  1  1  A  17  THR  A  17  .  ?        ?  
10  1  1  A  18  ILE  A  18  .  ?        1  
11  1  1  A  19  GLU  A  19  .  ?        ?  
12  1  1  A  20  ARG  A  20  .  ?        ?  
13  1  1  A  21  ASP  A  21  .  ?        ?  
14  1  1  A  22  GLY  A  22  .  ?        ?  
15  1  1  A  23  ARG  A  23  .  ?        ?  
16  1  1  A  24  LYS  A  24  .  ?        1  
17  1  1  A  25  VAL  A  25  .  ?        ?  
18  1  1  A  26  LYS  A  26  .  ?        ?  
19  1  1  A  27  LEU  A  27  .  ?        1  
20  1  1  A  28  VAL  A  28  .  ?        ?  
21  1  1  A  29  ARG  A  29  .  ?        ?  
22  1  1  A  30  ALA  A  30  .  ?        ?  
23  1  1  A  31  THR  A  31  .  ?        1  
24  1  1  A  32  ILE  A  32  .  ?        ?  
25  1  1  A  33  THR  A  33  .  ?        1  
26  1  1  A  34  VAL  A  34  .  ?        ?  
27  1  1  A  35  ASP  A  35  .  ?        ?  
28  1  1  A  36  PRO  A  36  .  ?        ?  
29  1  1  A  37  GLU  A  37  .  ?        ?  
30  1  1  A  38  THR  A  38  .  ?        ?  
31  1  1  A  39  ASN  A  39  .  ?        ?  
32  1  1  A  40  THR  A  40  .  ?        ?  
33  1  1  A  41  ILE  A  41  .  ?        ?  
34  1  1  A  42  THR  A  42  .  ?        1  
35  1  1  A  43  ILE  A  43  .  ?        ?  
36  1  1  A  44  ASP  A  44  .  ?        1  
37  1  1  A  45  ILE  A  45  .  ?        ?  
38  1  1  A  46  GLU  A  46  .  ?        ?  
39  1  1  A  47  TYR  A  47  .  ?        ?  
40  1  1  A  48  GLU  A  48  .  ?        ?  
41  1  1  A  49  GLY  A  49  .  ?        ?  
42  1  1  A  50  GLY  A  50  .  ?        1  
43  1  1  A  51  PRO  A  51  .  ?        ?  
44  1  1  A  52  ILE  A  52  .  ?        ?  
45  1  1  A  53  THR  A  53  .  ?        ?  
46  1  1  A  54  LYS  A  54  .  ?        ?  
47  1  1  A  55  GLU  A  55  .  ?        ?  
48  1  1  A  56  ASP  A  56  .  ?        ?  
49  1  1  A  57  LEU  A  57  .  ?        ?  
50  1  1  A  58  LEU  A  58  .  ?        ?  
51  1  1  A  59  GLU  A  59  .  ?        1  
52  1  1  A  60  ALA  A  60  .  ?        ?  
53  1  1  A  61  PHE  A  61  .  ?        ?  
54  1  1  A  62  LYS  A  62  .  ?        ?  
55  1  1  A  63  LEU  A  63  .  ?        ?  
56  1  1  A  64  ALA  A  64  .  ?        ?  
57  1  1  A  65  ALA  A  65  .  ?        ?  
58  1  1  A  66  SER  A  66  .  ?        ?  
59  1  1  A  67  LYS  A  67  .  ?        ?  
60  1  1  A  68  LEU  A  68  .  ?        ?  
#
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.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  Cg_endo       ?       ?  ?         7  82.130   8  0.15  11  0.22  molprobity  1.000  
 2   2  mp        -88.4   136.2  Favored  11  71.140   8  0.21  11  0.46  molprobity  1.000  
 3   3  t        -123.1   131.8  Favored   9  71.010   7  0.19  10  0.40  molprobity  1.000  
 4   4  mp       -128.1   127.0  Favored  11  72.250   8  0.19  11  0.43  molprobity  1.000  
 5   5  m-20      -75.3   135.7  Favored   4  88.400   8  0.19  11  0.28  molprobity  1.000  
 6   6  mt       -107.1   -67.9  Allowed  11  75.680   8  0.18  11  0.33  molprobity  1.000  
 7   7  m-20       58.7    46.2  Favored   6  86.190   8  0.25  11  0.43  molprobity  1.000  
 8   8  tptp     -136.8   147.6  Favored  13  78.210   9  0.23  11  0.42  molprobity  1.000  
 9   9  p        -112.2   155.3  Favored   7  70.090   7  0.18  10  0.71  molprobity  1.000  
10  10  mt       -137.3   117.0  Favored  11  71.940   8  0.20  11  0.48  molprobity  1.000  
11  11  mt-10    -105.4    59.2  Allowed   6  91.560   9  0.29  12  0.25  molprobity  1.000  
12  12  tpt180    -83.3   124.6  Favored  13  82.640  11  0.28  14  0.93  molprobity  1.000  
13  13  m-20       57.4    32.4  Favored   4  69.030   8  0.19  11  0.38  molprobity  1.000  
14  14  ?          82.8    12.1  Favored   3  72.040   4  0.33   5  0.75  molprobity  1.000  
15  15  OUTLIER  -107.2   114.1  Favored  13  74.410  11  0.25  14  1.00  molprobity  1.000  
16  16  mttt      -72.8   122.9  Favored  13  90.030   9  0.26  11  0.35  molprobity  1.000  
17  17  t        -134.2    90.9  Allowed   9  68.700   7  0.29  10  0.59  molprobity  1.000  
18  18  tmtm?     -84.3   115.7  Favored  13  77.670   9  0.24  11  0.38  molprobity  1.000  
19  19  mp        -77.2   147.2  Favored  11  65.760   8  0.21  11  0.79  molprobity  1.000  
20  20  t        -118.8   -54.8  Favored   9  65.660   7  0.20  10  0.29  molprobity  1.000  
21  21  ttm-85   -159.2   152.7  Favored  13  79.690  11  0.20  14  1.00  molprobity  1.000  
22  22  ?        -126.5   119.7  Favored   5  62.000   5  0.31   7  0.58  molprobity  1.000  
23  23  m        -105.8   104.8  Favored   7  67.170   7  0.22  10  0.66  molprobity  1.000  
24  24  mm        -91.7   131.4  Favored  11  65.520   8  0.21  11  0.38  molprobity  1.000  
25  25  m        -119.5   107.9  Favored   7  71.410   7  0.22  10  0.64  molprobity  1.000  
26  26  t        -100.1   127.8  Favored   9  63.930   7  0.28  10  0.38  molprobity  1.000  
27  27  t0       -120.8   101.5  Favored   4  80.610   8  0.33  12  0.39  molprobity  1.000  
28  28  Cg_endo   -71.7   -14.3  Favored   7  68.840   8  0.25  11  0.36  molprobity  1.000  
29  29  mt-10     -86.6   -19.4  Favored   6  90.590   9  0.23  12  0.37  molprobity  1.000  
30  30  p        -116.7     5.6  Favored   7  71.880   7  0.21  10  0.58  molprobity  1.000  
31  31  m-20       57.2    41.0  Favored   6  68.040   8  0.23  11  0.31  molprobity  1.000  
32  32  p        -126.7   137.6  Favored   7  69.320   7  0.22  10  0.63  molprobity  1.000  
33  33  mp       -115.6   122.1  Favored  11  60.760   8  0.23  11  0.52  molprobity  1.000  
34  34  m        -107.2   134.4  Favored   7  65.100   7  0.20  10  0.62  molprobity  1.000  
35  35  mt       -126.3   112.9  Favored  11  62.130   8  0.26  11  0.42  molprobity  1.000  
36  36  t0        -90.8   133.2  Favored   4  82.160   8  0.23  11  0.42  molprobity  1.000  
37  37  mt       -126.4   112.1  Favored  11  61.190   8  0.27  11  0.43  molprobity  1.000  
38  38  mp0       -95.2   135.5  Favored   6  70.240   9  0.22  12  0.36  molprobity  1.000  
39  39  p90      -144.3   145.4  Favored   9  62.120  13  0.26  18  0.33  molprobity  1.000  
40  40  tm-20    -110.1    89.7  Favored   6  89.570   9  0.20  12  0.64  molprobity  1.000  
41  41  ?        -170.6  -168.4  Favored   3  75.110   4  0.37   5  0.49  molprobity  1.000  
42  42  ?         -68.8  -167.0  Favored   3  81.740   4  0.47   6  0.38  molprobity  1.000  
43  43  Cg_endo   -68.8   131.4  Favored   7  86.720   8  0.18  11  0.32  molprobity  1.000  
44  44  tt        -94.6   157.6  Favored  11  67.370   8  0.20  11  0.42  molprobity  1.000  
45  45  p        -130.5  -178.0  Favored   7  62.040   7  0.18  10  0.61  molprobity  1.000  
46  46  mttt      -70.8   -34.5  Favored  13  71.140   9  0.24  11  0.24  molprobity  1.000  
47  47  mt-10     -65.2   -37.1  Favored   6  80.540   9  0.20  12  0.31  molprobity  0.820  
48  48  m-20      -73.5   -33.4  Favored   4  65.400   8  0.18  11  0.29  molprobity  1.000  
49  49  mt        -67.9   -32.5  Favored  11  55.880   8  0.21  11  0.28  molprobity  1.000  
50  50  mt        -69.3   -29.4  Favored  11  55.360   8  0.20  11  0.23  molprobity  1.000  
51  51  tp10      -69.3   -47.8  Favored   6  75.630   9  0.20  12  0.33  molprobity  1.000  
52  52  ?         -65.5   -23.7  Favored   5  72.070   5  0.24   7  0.18  molprobity  1.000  
53  53  t80       -70.9   -33.7  Favored   9  65.210  12  0.33  16  0.35  molprobity  1.000  
54  54  mttt      -69.4   -41.8  Favored  13  81.470   9  0.25  11  0.44  molprobity  1.000  
55  55  tp        -68.4   -38.8  Favored  11  73.340   8  0.23  11  0.23  molprobity  1.000  
56  56  ?         -63.9   -36.3  Favored   5  73.170   5  0.24   7  0.29  molprobity  1.000  
57  57  ?         -71.9   -35.1  Favored   5  76.110   5  0.22   7  0.22  molprobity  1.000  
58  58  p         -69.8   -14.9  Favored   5  84.320   6  0.23   8  0.42  molprobity  1.000  
59  59  mmtt      -95.7     6.1  Favored  13  97.550   9  0.22  11  0.35  molprobity  1.000  
60  60  pp            ?       ?  ?        11  92.060   7  0.26   8  0.97  molprobity  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   6  HD13  1  0.41  2.02  
 2  10  HD13  2  0.42  2.01  
 3  16  O     3  0.54  2.36  
 4  19  HD23  1  0.41  2.02  
 5  23  HB    4  0.49  1.93  
 6  25  HB    5  0.40  2.03  
 7  34  HB    5  0.40  2.03  
 8  36  HB3   4  0.49  1.93  
 9  42  N     3  0.54  2.36  
10  51  HB3   2  0.42  2.01  
#
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   7  0.792  0.151   0.047  
 2   2   8  0.970  0.162  -0.065  
 3   3   7  0.934  0.107  -0.886  
 4   4   8  0.952  0.183   0.286  
 5   5   8  0.882  0.280   1.652  
 6   6   8  0.949  0.268   1.633  
 7   7   8  0.879  0.159  -0.015  
 8   8   9  0.882  0.196  -0.031  
 9   9   7  0.939  0.138  -0.227  
10  10   8  0.931  0.152  -0.232  
11  11   9  0.905  0.153  -0.443  
12  12  11  0.927  0.223   0.525  
13  13   8  0.944  0.141  -0.306  
14  14   4  0.933  0.134  -0.166  
15  15  11  0.940  0.150  -0.443  
16  16   9  0.948  0.217   0.229  
17  17   7  0.956  0.133  -0.451  
18  18   9  0.957  0.223   0.304  
19  19   8  0.962  0.164  -0.064  
20  20   7  0.929  0.127  -0.551  
21  21  11  0.940  0.190   0.088  
22  22   5  0.970  0.151   0.037  
23  23   7  0.974  0.111  -0.666  
24  24   8  0.971  0.108  -0.968  
25  25   7  0.959  0.100  -0.844  
26  26   7  0.969  0.146  -0.233  
27  27   8  0.925  0.127  -0.503  
28  28   7  0.975  0.163   0.234  
29  29   9  0.888  0.173  -0.195  
30  30   7  0.965  0.110  -0.682  
31  31   8  0.966  0.118  -0.617  
32  32   7  0.948  0.085  -1.088  
33  33   8  0.929  0.146  -0.333  
34  34   7  0.971  0.085  -1.088  
35  35   8  0.970  0.147  -0.316  
36  36   8  0.909  0.263   1.413  
37  37   8  0.955  0.164  -0.032  
38  38   9  0.943  0.176  -0.158  
39  39  12  0.947  0.134  -0.330  
40  40   9  0.846  0.293   1.296  
41  41   4  0.928  0.109  -0.534  
42  42   4  0.938  0.136  -0.137  
43  43   7  0.917  0.153   0.078  
44  44   8  0.881  0.180   0.236  
45  45   7  0.961  0.105  -0.763  
46  46   9  0.954  0.215   0.204  
47  47   9  0.885  0.228   0.488  
48  48   8  0.901  0.150  -0.179  
49  49   8  0.961  0.162  -0.096  
50  50   8  0.964  0.117  -0.830  
51  51   9  0.961  0.219   0.376  
52  52   5  0.957  0.174   0.410  
53  53  11  0.906  0.164   0.097  
54  54   9  0.969  0.197  -0.019  
55  55   8  0.970  0.261   1.519  
56  56   5  0.985  0.154   0.086  
57  57   5  0.971  0.153   0.070  
58  58   6  0.953  0.132  -0.287  
59  59   9  0.948  0.174  -0.304  
60  60   8  0.908  0.248   1.307  
#
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  eds          2.29                                                                  Y  
3  dcc          "2.26  (2020-01-20)"                                                  Y  
4  xtriage      1.13                                                                  Y  
5  percentiles  "20191225.v01 (using entries in the PDB archive December 25th 2019)"  Y  
##
