data_4YMC

_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  4YMC
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    4YMC
_pdbx_vrpt_summary.PDB_deposition_date         2015-03-06
_pdbx_vrpt_summary.PDB_revision_number         3
_pdbx_vrpt_summary.PDB_revision_date           2024-05-08
_pdbx_vrpt_summary.report_creation_date        2024-04-29:10:41
_pdbx_vrpt_summary.attempted_validation_steps  molprobity,validation-pack,xtriage,eds,mogul,buster-report,percentiles,writexml,writecif,writepdf
_pdbx_vrpt_summary.ligands_for_buster_report   Y
#
loop_
_pdbx_vrpt_entity.id
_pdbx_vrpt_entity.type
_pdbx_vrpt_entity.description
1  polymer      "DNA (5'-D(*CP*CP*GP*GP*AP*TP*CP*CP*GP*G)-3')"  
2  non-polymer  "BARIUM ION"  
3  non-polymer  "Ru(tap)2(dppz) complex"  
4  non-polymer  "CHLORIDE ION"  
5  water        water  
#
loop_
_pdbx_vrpt_asym.label_asym_id
_pdbx_vrpt_asym.entity_id
A  1  
B  2  
C  3  
D  4  
E  5  
#
loop_
_pdbx_vrpt_percentile_list.id
_pdbx_vrpt_percentile_list.range
_pdbx_vrpt_percentile_list.exp_method
1  all   x-ray  
2  1.88  x-ray  
#
loop_
_pdbx_vrpt_percentile_type.id
_pdbx_vrpt_percentile_type.type
1  all_atom_clashscore    
2  RSRZ_outliers_percent  
3  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   81.14  141614     ?     ?  
2  2  1   77.99   10282  1.86  1.90  
3  1  2  100.00  127900     ?     ?  
4  2  2  100.00    9303  1.86  1.90  
5  1  3   27.11  130704     ?     ?  
6  2  3   12.49    9470  1.86  1.90  
#
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  
#
_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      0.95
_pdbx_vrpt_summary_entity_geometry.bonds_RMSZ       0.74
_pdbx_vrpt_summary_entity_geometry.num_bonds_RMSZ   226
_pdbx_vrpt_summary_entity_geometry.num_angles_RMSZ  347
#
_pdbx_vrpt_summary_geometry.ordinal          1
_pdbx_vrpt_summary_geometry.clashscore       2.56
_pdbx_vrpt_summary_geometry.num_H_reduce     135
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ   226
_pdbx_vrpt_summary_geometry.bonds_RMSZ       0.74
_pdbx_vrpt_summary_geometry.num_angles_RMSZ  347
_pdbx_vrpt_summary_geometry.angles_RMSZ      0.95
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.Babinet_b                 75.909
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            38.073
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         44.291
_pdbx_vrpt_summary_diffraction.I_over_sigma              1.49(1.88A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        3399
_pdbx_vrpt_summary_diffraction.Babinet_k                 0.289
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.302
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.481
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.316
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.973
_pdbx_vrpt_summary_diffraction.DCC_R                     0.20
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.26
_pdbx_vrpt_summary_diffraction.EDS_R                     0.20
_pdbx_vrpt_summary_diffraction.EDS_res_high              1.88
_pdbx_vrpt_summary_diffraction.EDS_res_low               27.53
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[44.192,44.192,44.531,0.000,0.000,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.008
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The largest off-origin peak in the Patterson function is 16.67% 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         99.88
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      149
_pdbx_vrpt_summary_diffraction.percent_free_reflections  4.38
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     0.00
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       1.88
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        33.83
_pdbx_vrpt_summary_diffraction.PDB_R                     0.20
_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_angle_outliers
_pdbx_vrpt_model_instance.count_clashes
_pdbx_vrpt_model_instance.count_mogul_bond_outliers
_pdbx_vrpt_model_instance.count_mogul_angle_outliers
 1  1  1  A   1  DC   A    1  .  ?        1     ?     ?     ?  
 2  1  1  A   2  DC   A    2  .  ?        ?     ?     ?     ?  
 3  1  1  A   3  DG   A    3  .  ?        ?     ?     ?     ?  
 4  1  1  A   4  DG   A    4  .  ?        ?     ?     ?     ?  
 5  1  1  A   5  DA   A    5  .  ?        ?     ?     ?     ?  
 6  1  1  A   6  DT   A    6  .  ?        ?     ?     ?     ?  
 7  1  1  A   7  DC   A    7  .  ?        ?     ?     ?     ?  
 8  1  1  A   8  DC   A    8  .  ?        ?     ?     ?     ?  
 9  1  1  A   9  DG   A    9  .  ?        ?     ?     ?     ?  
10  1  1  A  10  DG   A   10  .  ?        ?     2     ?     ?  
11  1  2  B   .  BA   A  101  .  ?        ?     ?     ?     ?  
12  1  3  C   .  RKL  A  102  .  ?        ?     ?    11    19  
13  1  4  D   .  CL   A  103  .  ?        ?     ?     ?     ?  
14  1  5  E   .  HOH  A  201  .  ?        ?     ?     ?     ?  
15  1  5  E   .  HOH  A  202  .  ?        ?     ?     ?     ?  
16  1  5  E   .  HOH  A  203  .  ?        ?     ?     ?     ?  
17  1  5  E   .  HOH  A  204  .  ?        ?     ?     ?     ?  
18  1  5  E   .  HOH  A  205  .  ?        ?     ?     ?     ?  
19  1  5  E   .  HOH  A  206  .  ?        ?     ?     ?     ?  
20  1  5  E   .  HOH  A  207  .  ?        ?     ?     ?     ?  
21  1  5  E   .  HOH  A  208  .  ?        ?     ?     ?     ?  
22  1  5  E   .  HOH  A  209  .  ?        ?     ?     ?     ?  
23  1  5  E   .  HOH  A  210  .  ?        ?     ?     ?     ?  
24  1  5  E   .  HOH  A  211  .  ?        ?     ?     ?     ?  
25  1  5  E   .  HOH  A  212  .  ?        ?     ?     ?     ?  
26  1  5  E   .  HOH  A  213  .  ?        ?     ?     ?     ?  
27  1  5  E   .  HOH  A  214  .  ?        ?     ?     ?     ?  
28  1  5  E   .  HOH  A  215  .  ?        ?     ?     ?     ?  
29  1  5  E   .  HOH  A  216  .  ?        ?     ?     ?     ?  
30  1  5  E   .  HOH  A  217  .  ?        ?     ?     ?     ?  
31  1  5  E   .  HOH  A  218  .  ?        ?     ?     ?     ?  
32  1  5  E   .  HOH  A  219  .  ?        ?     ?     ?     ?  
33  1  5  E   .  HOH  A  220  .  ?        ?     ?     ?     ?  
#
loop_
_pdbx_vrpt_model_instance_geometry.ordinal
_pdbx_vrpt_model_instance_geometry.instance_id
_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    12  74.000    18  0.30    28  1.58  molprobity  1.000  
 2   2    11  52.380    21  0.87    32  1.11  molprobity  1.000  
 3   3    11  40.480    25  0.59    39  0.95  molprobity  1.000  
 4   4    11  43.760    25  0.63    39  0.69  molprobity  1.000  
 5   5    11  48.570    24  0.89    37  1.20  molprobity  1.000  
 6   6    12  56.040    22  0.69    34  0.81  molprobity  1.000  
 7   7    11  50.150    21  0.55    32  0.73  molprobity  1.000  
 8   8    11  40.250    21  1.03    32  0.73  molprobity  1.000  
 9   9    11  41.940    25  0.81    39  0.86  molprobity  1.000  
10  10    12  53.080    24  0.70    35  0.56  molprobity  1.000  
11  11     ?  46.540     ?     ?     ?     ?  ?           1.000  
12  12    22  38.970    64  1.50    82  1.51  mogul       1.000  
13  13     ?  61.900     ?     ?     ?     ?  ?           1.000  
14  14     ?  45.180     ?     ?     ?     ?  ?           1.000  
15  15     ?  44.270     ?     ?     ?     ?  ?           1.000  
16  16     ?  54.450     ?     ?     ?     ?  ?           1.000  
17  17     ?  35.120     ?     ?     ?     ?  ?           1.000  
18  18     ?  49.870     ?     ?     ?     ?  ?           1.000  
19  19     ?  45.410     ?     ?     ?     ?  ?           1.000  
20  20     ?  43.410     ?     ?     ?     ?  ?           1.000  
21  21     ?  50.020     ?     ?     ?     ?  ?           1.000  
22  22     ?  53.030     ?     ?     ?     ?  ?           1.000  
23  23     ?  59.270     ?     ?     ?     ?  ?           1.000  
24  24     ?  45.180     ?     ?     ?     ?  ?           1.000  
25  25     ?  49.290     ?     ?     ?     ?  ?           1.000  
26  26     ?  47.890     ?     ?     ?     ?  ?           0.500  
27  27     ?  51.480     ?     ?     ?     ?  ?           1.000  
28  28     ?  47.420     ?     ?     ?     ?  ?           1.000  
29  29     ?  40.120     ?     ?     ?     ?  ?           1.000  
30  30     ?  49.190     ?     ?     ?     ?  ?           1.000  
31  31     ?  50.460     ?     ?     ?     ?  ?           1.000  
32  32     ?  53.700     ?     ?     ?     ?  ?           1.000  
33  33     ?  53.700     ?     ?     ?     ?  ?           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  10  N3     1  0.50  2.26  
2  10  "H3'"  1  0.50  2.26  
#
_pdbx_vrpt_instance_intra_angle_outliers.ordinal      1
_pdbx_vrpt_instance_intra_angle_outliers.instance_id  1
_pdbx_vrpt_instance_intra_angle_outliers.atom_1       "C5'"
_pdbx_vrpt_instance_intra_angle_outliers.atom_2       "C4'"
_pdbx_vrpt_instance_intra_angle_outliers.atom_3       "O4'"
_pdbx_vrpt_instance_intra_angle_outliers.obs          122.212
_pdbx_vrpt_instance_intra_angle_outliers.mean         109.300
_pdbx_vrpt_instance_intra_angle_outliers.stdev        1.900
_pdbx_vrpt_instance_intra_angle_outliers.Z            6.80
#
loop_
_pdbx_vrpt_instance_mogul_bond_outliers.ordinal
_pdbx_vrpt_instance_mogul_bond_outliers.instance_id
_pdbx_vrpt_instance_mogul_bond_outliers.atom_1
_pdbx_vrpt_instance_mogul_bond_outliers.atom_2
_pdbx_vrpt_instance_mogul_bond_outliers.obsval
_pdbx_vrpt_instance_mogul_bond_outliers.mean
_pdbx_vrpt_instance_mogul_bond_outliers.numobs
_pdbx_vrpt_instance_mogul_bond_outliers.stdev
_pdbx_vrpt_instance_mogul_bond_outliers.Zscore
_pdbx_vrpt_instance_mogul_bond_outliers.mindiff
 1  12  RU   N9   1.99  2.06   1188  0.04  -2.08  0.00  
 2  12  C5   C6   1.37  1.45   2831  0.02  -3.98  0.00  
 3  12  C8   C7   1.38  1.45   2831  0.02  -3.17  0.00  
 4  12  C26  N8   1.32  1.37   1931  0.02  -2.31  0.00  
 5  12  C29  N9   1.32  1.37   1931  0.02  -2.29  0.00  
 6  12  C31  N10  1.26  1.32   6831  0.02  -2.98  0.00  
 7  12  C15  C13  1.37  1.42   2926  0.02  -2.59  0.00  
 8  12  C16  C15  1.37  1.41  10000  0.02  -2.46  0.00  
 9  12  C24  C25  1.38  1.41  10000  0.02  -2.05  0.00  
10  12  C33  C32  1.35  1.41  10000  0.02  -3.43  0.00  
11  12  C34  C35  1.36  1.41  10000  0.02  -3.07  0.00  
#
loop_
_pdbx_vrpt_instance_mogul_angle_outliers.ordinal
_pdbx_vrpt_instance_mogul_angle_outliers.instance_id
_pdbx_vrpt_instance_mogul_angle_outliers.atom_1
_pdbx_vrpt_instance_mogul_angle_outliers.atom_2
_pdbx_vrpt_instance_mogul_angle_outliers.atom_3
_pdbx_vrpt_instance_mogul_angle_outliers.obsval
_pdbx_vrpt_instance_mogul_angle_outliers.mean
_pdbx_vrpt_instance_mogul_angle_outliers.numobs
_pdbx_vrpt_instance_mogul_angle_outliers.stdev
_pdbx_vrpt_instance_mogul_angle_outliers.Zscore
_pdbx_vrpt_instance_mogul_angle_outliers.mindiff
 1  12  C5   C1   N2   120.58  122.78    264  0.96  -2.29  0.03  
 2  12  C10  C1   N2   119.36  116.56   1918  1.35   2.06  0.01  
 3  12  C6   N3   C15  119.47  116.77   1279  1.00   2.70  0.01  
 4  12  C3   C4   C5   117.49  120.86  10000  1.68  -2.00  0.00  
 5  12  C7   N4   C13  120.27  116.77   1279  1.00   3.50  0.01  
 6  12  C4   C5   C6   119.54  122.55   2333  1.42  -2.12  0.00  
 7  12  C6   C7   N4   118.46  121.83   1421  0.91  -3.71  0.03  
 8  12  C8   C7   N4   121.27  118.36   1438  1.02   2.85  0.00  
 9  12  C27  N7   C25  120.89  116.93   1679  1.55   2.56  0.15  
10  12  C28  N8   C26  121.94  117.51   1855  2.20   2.02  0.05  
11  12  C1   C10  N1   119.50  116.56   1918  1.35   2.17  0.00  
12  12  C8   C10  C1   118.31  120.67   1803  1.02  -2.30  0.05  
13  12  C11  C12  N1   118.55  122.71   1956  2.02  -2.06  0.00  
14  12  C13  C15  N3   119.27  121.42   2652  0.83  -2.58  0.02  
15  12  C26  C19  N5   119.68  116.56   1918  1.35   2.30  0.09  
16  12  C19  C26  N8   120.05  116.56   1918  1.35   2.58  0.03  
17  12  C28  C27  N7   119.91  123.29    176  1.54  -2.20  0.45  
18  12  C36  C29  N9   121.00  116.56   1918  1.35   3.28  0.12  
19  12  C29  C36  N12  119.28  116.56   1918  1.35   2.01  0.00  
#
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  16  0.878  0.241   1.710  
 2   2  19  0.891  0.130   0.018  
 3   3  22  0.970  0.087  -0.635  
 4   4  22  0.955  0.091  -0.567  
 5   5  21  0.931  0.090  -0.577  
 6   6  20  0.877  0.119  -0.154  
 7   7  19  0.925  0.103  -0.393  
 8   8  19  0.967  0.086  -0.652  
 9   9  22  0.955  0.110  -0.247  
10  10  22  0.844  0.170   0.763  
11  11   1  0.988  0.160       ?  
12  12  51  0.985  0.116       ?  
13  13   1  0.971  0.095       ?  
14  14   1  0.923  0.169       ?  
15  15   1  0.820  0.140       ?  
16  16   1  0.758  0.196       ?  
17  17   1  0.804  0.161       ?  
18  18   1  0.894  0.139       ?  
19  19   1  0.915  0.175       ?  
20  20   1  0.875  0.324       ?  
21  21   1  0.959  0.106       ?  
22  22   1  0.892  0.148       ?  
23  23   1  0.501  0.504       ?  
24  24   1  0.854  0.323       ?  
25  25   1  0.886  0.278       ?  
26  26   1  0.940  0.334       ?  
27  27   1  0.816  0.411       ?  
28  28   1  0.897  0.411       ?  
29  29   1  0.860  0.199       ?  
30  30   1  0.528  0.260       ?  
31  31   1  0.942  0.207       ?  
32  32   1  0.912  0.167       ?  
33  33   1  0.878  0.191       ?  
#
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        "1.8.4, CSD as541be (2020)"                                           Y  
3  eds          2.36.2                                                                Y  
4  dcc          '"2.27  (2023-04-10)"'                                                Y  
5  xtriage      1.13                                                                  Y  
6  percentiles  "20191225.v01 (using entries in the PDB archive December 25th 2019)"  Y  
##
