data_6F3C

_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  6F3C
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    6F3C
_pdbx_vrpt_summary.PDB_deposition_date         2017-11-28
_pdbx_vrpt_summary.PDB_revision_number         4
_pdbx_vrpt_summary.PDB_revision_date           2024-01-17
_pdbx_vrpt_summary.report_creation_date        2024-01-06:19:25
_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(*GP*TP*AP*CP*G)-3')"  
2  polymer      "DNA (5'-D(*GP*TP*AP*CP*G)-3')"  
3  non-polymer  "MAGNESIUM ION"  
4  non-polymer  "[Pt(H2bapbpy)] platinum"  
5  water        water  
#
loop_
_pdbx_vrpt_asym.label_asym_id
_pdbx_vrpt_asym.entity_id
A  1  
B  1  
C  2  
D  2  
E  3  
F  4  
G  4  
H  5  
I  5  
J  5  
#
loop_
_pdbx_vrpt_percentile_list.id
_pdbx_vrpt_percentile_list.range
_pdbx_vrpt_percentile_list.exp_method
1  all  x-ray  
2  2.3  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   5.11  141614     ?     ?  
2  2  1   4.57    5643  2.30  2.30  
3  1  2  32.89  127900     ?     ?  
4  2  2  39.81    4938  2.30  2.30  
5  1  3   3.26  130704     ?     ?  
6  2  3   2.51    5042  2.30  2.30  
#
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  B  100.00  
2  4  2  A  1  1  B  100.00  
3  3  2  B  1  1  D    1.22  
4  4  2  B  1  1  D    1.72  
5  3  2  C  1  2  C  100.00  
6  4  2  C  1  2  C  100.00  
7  3  2  D  1  2  A  100.00  
8  4  2  D  1  2  A  100.00  
#
loop_
_pdbx_vrpt_summary_entity_geometry.ordinal
_pdbx_vrpt_summary_entity_geometry.PDB_model_num
_pdbx_vrpt_summary_entity_geometry.entity_id
_pdbx_vrpt_summary_entity_geometry.label_asym_id
_pdbx_vrpt_summary_entity_geometry.auth_asym_id
_pdbx_vrpt_summary_entity_geometry.angles_RMSZ
_pdbx_vrpt_summary_entity_geometry.bonds_RMSZ
_pdbx_vrpt_summary_entity_geometry.num_bonds_RMSZ
_pdbx_vrpt_summary_entity_geometry.num_angles_RMSZ
1  1  1  A  B  0.98  0.60  134  205  
2  1  1  B  D  1.00  0.57  134  205  
3  1  2  C  C  0.94  0.57  113  173  
4  1  2  D  A  1.00  0.63  113  173  
#
_pdbx_vrpt_summary_geometry.ordinal          1
_pdbx_vrpt_summary_geometry.clashscore       26.63
_pdbx_vrpt_summary_geometry.num_H_reduce     254
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ   494
_pdbx_vrpt_summary_geometry.bonds_RMSZ       0.59
_pdbx_vrpt_summary_geometry.num_angles_RMSZ  756
_pdbx_vrpt_summary_geometry.angles_RMSZ      0.98
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.Babinet_b                 87.563
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            40.238
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         71.272
_pdbx_vrpt_summary_diffraction.I_over_sigma              1.47(2.29A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        3084
_pdbx_vrpt_summary_diffraction.Babinet_k                 0.511
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.313
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.525
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.376
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.940
_pdbx_vrpt_summary_diffraction.twin_fraction             -h,-k,l:0.037
_pdbx_vrpt_summary_diffraction.DCC_R                     0.28
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.31
_pdbx_vrpt_summary_diffraction.EDS_R                     0.27
_pdbx_vrpt_summary_diffraction.EDS_res_high              2.30
_pdbx_vrpt_summary_diffraction.EDS_res_low               39.00
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[70.111,70.111,72.372,0.000,0.000,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.032
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The largest off-origin peak in the Patterson function is 18.37% 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         8
_pdbx_vrpt_summary_diffraction.centric_outliers          0
_pdbx_vrpt_summary_diffraction.data_completeness         98.06
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      347
_pdbx_vrpt_summary_diffraction.percent_free_reflections  11.25
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     4.55
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       2.30
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        39.00
_pdbx_vrpt_summary_diffraction.PDB_R                     0.26
_pdbx_vrpt_summary_diffraction.PDB_Rfree                 0.29
#
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
_pdbx_vrpt_model_instance.count_mogul_bond_outliers
_pdbx_vrpt_model_instance.count_mogul_angle_outliers
_pdbx_vrpt_model_instance.ligand_of_interest
 1  1  1  A  1  DC   B    7  .  ?        1     ?     ?  ?     
 2  1  1  A  2  DG   B    8  .  ?        3     ?     ?  ?     
 3  1  1  A  3  DT   B    9  .  ?        1     ?     ?  ?     
 4  1  1  A  4  DA   B   10  .  ?        ?     ?     ?  ?     
 5  1  1  A  5  DC   B   11  .  ?        ?     ?     ?  ?     
 6  1  1  A  6  DG   B   12  .  ?        1     ?     ?  ?     
 7  1  1  B  1  DC   D    7  .  ?        ?     ?     ?  ?     
 8  1  1  B  2  DG   D    8  .  ?        ?     ?     ?  ?     
 9  1  1  B  3  DT   D    9  .  ?        1     ?     ?  ?     
10  1  1  B  4  DA   D   10  .  ?        1     ?     ?  ?     
11  1  1  B  5  DC   D   11  .  ?        ?     ?     ?  ?     
12  1  1  B  6  DG   D   12  .  ?        ?     ?     ?  ?     
13  1  2  C  1  DG   C    2  .  ?        2     ?     ?  ?     
14  1  2  C  2  DT   C    3  .  ?        4     ?     ?  ?     
15  1  2  C  3  DA   C    4  .  ?        2     ?     ?  ?     
16  1  2  C  4  DC   C    5  .  ?        ?     ?     ?  ?     
17  1  2  C  5  DG   C    6  .  ?        ?     ?     ?  ?     
18  1  2  D  1  DG   A    2  .  ?        1     ?     ?  ?     
19  1  2  D  2  DT   A    3  .  ?        2     ?     ?  ?     
20  1  2  D  3  DA   A    4  .  ?        1     ?     ?  ?     
21  1  2  D  4  DC   A    5  .  ?        2     ?     ?  ?     
22  1  2  D  5  DG   A    6  .  ?        ?     ?     ?  ?     
23  1  3  E  .  MG   B  101  .  ?        ?     ?     ?  ?     
24  1  4  F  .  PT9  A  101  A  ?        3    12    13  Y     
25  1  4  G  .  PT9  A  102  B  ?        2     9    16  Y     
26  1  5  H  .  HOH  B  201  .  ?        ?     ?     ?  ?     
27  1  5  H  .  HOH  B  202  .  ?        1     ?     ?  ?     
28  1  5  H  .  HOH  B  203  .  ?        ?     ?     ?  ?     
29  1  5  H  .  HOH  B  204  .  ?        ?     ?     ?  ?     
30  1  5  I  .  HOH  C  101  .  ?        ?     ?     ?  ?     
31  1  5  I  .  HOH  C  102  .  ?        ?     ?     ?  ?     
32  1  5  J  .  HOH  A  201  .  ?        ?     ?     ?  ?     
33  1  5  J  .  HOH  A  202  .  ?        ?     ?     ?  ?     
34  1  5  J  .  HOH  A  203  .  ?        ?     ?     ?  ?     
#
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  87.540    18  0.33    28  0.69  molprobity  1.000  
 2   2    11  46.960    25  0.68    39  1.15  molprobity  1.000  
 3   3    12  51.270    22  0.54    34  1.00  molprobity  1.000  
 4   4    11  51.200    24  0.57    37  0.76  molprobity  1.000  
 5   5    11  50.330    21  0.82    32  1.15  molprobity  1.000  
 6   6    12  53.550    24  0.51    35  0.98  molprobity  1.000  
 7   7    12  86.870    18  0.35    28  0.60  molprobity  1.000  
 8   8    11  46.890    25  0.68    39  0.99  molprobity  1.000  
 9   9    12  48.810    22  0.49    34  1.04  molprobity  1.000  
10  10    11  50.320    24  0.68    37  0.79  molprobity  1.000  
11  11    11  52.110    21  0.66    32  1.51  molprobity  1.000  
12  12    12  58.490    24  0.42    35  0.83  molprobity  1.000  
13  13    12  53.570    22  0.71    35  1.00  molprobity  1.000  
14  14    12  63.050    22  0.64    34  1.19  molprobity  1.000  
15  15    11  54.760    24  0.63    37  0.64  molprobity  1.000  
16  16    11  78.490    21  0.46    32  0.92  molprobity  1.000  
17  17    12  96.190    24  0.34    35  0.90  molprobity  1.000  
18  18    12  46.320    22  0.63    35  1.04  molprobity  1.000  
19  19    12  72.570    22  0.51    34  1.22  molprobity  1.000  
20  20    11  69.100    24  0.53    37  0.83  molprobity  1.000  
21  21    11  64.090    21  0.84    32  1.04  molprobity  1.000  
22  22    12  59.800    24  0.61    35  0.82  molprobity  1.000  
23  23     ?  37.300     ?     ?     ?     ?  ?           1.000  
24  24     ?  38.600    33  2.39    38  2.79  mogul       0.500  
25  25     ?  42.650    33  2.43    38  2.79  mogul       0.500  
26  26     ?  32.880     ?     ?     ?     ?  ?           1.000  
27  27     ?  81.860     ?     ?     ?     ?  ?           1.000  
28  28     ?  41.530     ?     ?     ?     ?  ?           1.000  
29  29     ?  80.260     ?     ?     ?     ?  ?           0.500  
30  30     ?  44.190     ?     ?     ?     ?  ?           1.000  
31  31     ?  48.460     ?     ?     ?     ?  ?           1.000  
32  32     ?  73.200     ?     ?     ?     ?  ?           1.000  
33  33     ?  45.750     ?     ?     ?     ?  ?           1.000  
34  34     ?  52.450     ?     ?     ?     ?  ?           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   1  "H4'"    1  0.74  1.68  
 2   2  "H5''"   1  0.74  1.68  
 3   2  O6       2  0.47  2.48  
 4   2  "H2'"    3  0.43  2.53  
 5   3  C6       3  0.43  2.53  
 6   6  "H5''"   4  0.80  1.82  
 7   9  "H2''"   5  0.41  2.55  
 8  10  C8       5  0.41  2.55  
 9  13  "H2''"   6  0.47  2.14  
10  13  "H2'"    7  0.43  1.99  
11  14  OP2      6  0.47  2.14  
12  14  "H2''"   8  0.46  2.16  
13  14  "H2''"   9  0.46  1.97  
14  14  H71      7  0.43  1.99  
15  15  OP2      8  0.46  2.16  
16  15  "H5'"    9  0.46  1.97  
17  18  "H2''"  10  0.62  2.35  
18  19  C6      10  0.62  2.35  
19  19  "H2''"  11  0.52  2.45  
20  20  C8      11  0.52  2.45  
21  21  "H2'"   12  0.80  2.11  
22  21  N3       2  0.47  2.48  
23  24  C8      12  0.80  2.11  
24  24  C20     13  0.56  2.84  
25  24  C1      13  0.56  2.84  
26  25  C20     14  0.77  2.63  
27  25  C1      14  0.77  2.63  
28  27  O        4  0.80  1.82  
#
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  24  C15  N4   1.31  1.35     74  0.01  -3.58  0.01  
 2  24  C5   N1   1.42  1.35     68  0.01   6.59  0.03  
 3  24  C5   N2   1.33  1.38   2845  0.02  -2.65  0.00  
 4  24  C6   N2   1.27  1.38   2845  0.02  -5.38  0.00  
 5  24  C8   C7   1.33  1.38  10000  0.02  -2.43  0.00  
 6  24  C9   C10  1.35  1.39  10000  0.02  -2.14  0.00  
 7  24  PT1  N1   2.04  2.02     30  0.01   3.34  0.00  
 8  24  PT1  N6   2.05  2.02     30  0.01   5.23  0.01  
 9  24  C3   C4   1.34  1.38  10000  0.02  -2.27  0.00  
10  24  C13  C14  1.34  1.38  10000  0.02  -2.10  0.00  
11  24  C15  N5   1.34  1.38   2845  0.02  -2.24  0.00  
12  24  C16  N6   1.31  1.35     68  0.01  -3.50  0.01  
13  25  C1   C2   1.33  1.38  10000  0.02  -2.23  0.00  
14  25  C11  N4   1.41  1.35   1476  0.02   2.40  0.00  
15  25  C15  N4   1.30  1.35     74  0.01  -4.09  0.01  
16  25  C5   N1   1.38  1.35     68  0.01   3.06  0.01  
17  25  C6   N2   1.31  1.38   2845  0.02  -3.75  0.00  
18  25  C9   C10  1.35  1.39  10000  0.02  -2.13  0.00  
19  25  PT1  N1   1.97  2.02     30  0.01  -7.33  0.04  
20  25  PT1  N6   2.06  2.02     30  0.01   7.65  0.03  
21  25  C16  N6   1.32  1.35     68  0.01  -2.48  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  24  C4   C5   N1   124.01  121.28     68  0.88   3.09  0.08  
 2  24  C4   C5   N2   108.33  117.63   2755  1.34  -6.95  0.64  
 3  24  N2   C5   N1   127.62  119.92     63  1.25   6.16  3.82  
 4  24  N2   C6   N3   129.57  120.02     67  1.30   7.37  5.78  
 5  24  C7   C6   N2   107.86  117.63   2755  1.34  -7.31  0.79  
 6  24  C11  C10  N3   116.67  112.90   1034  1.79   2.11  0.00  
 7  24  C13  C12  C11  116.27  119.25  10000  1.48  -2.01  0.00  
 8  24  N5   C15  N4   123.46  120.02     67  1.30   2.65  0.00  
 9  24  C17  C16  N5   113.38  117.63   2755  1.34  -3.18  0.00  
10  24  C17  C16  N6   123.99  121.28     68  0.88   3.08  0.09  
11  24  N5   C16  N6   122.63  119.92     63  1.25   2.17  0.68  
12  24  C1   N1   C5   114.12  118.04     66  1.08  -3.64  0.58  
13  24  C6   N2   C5   119.81  130.33   1384  3.23  -3.26  0.31  
14  25  C1   C2   C3   114.91  118.85  10000  1.50  -2.63  0.00  
15  25  C4   C5   N1   114.86  121.28     68  0.88  -7.28  3.30  
16  25  N2   C5   N1   127.71  119.92     63  1.25   6.23  3.92  
17  25  C7   C6   N3   118.14  121.23     79  0.85  -3.63  0.03  
18  25  N2   C6   N3   126.27  120.02     67  1.30   4.82  2.47  
19  25  C8   C9   C10  116.19  119.25  10000  1.48  -2.07  0.00  
20  25  C2   C1   N1   128.16  122.04   3637  1.68   3.63  0.03  
21  25  C3   C4   C5   123.04  118.96   4982  1.27   3.22  0.05  
22  25  C9   C10  N3   124.44  119.12    838  1.89   2.82  0.30  
23  25  C12  C11  N4   126.68  119.12    838  1.89   4.01  0.96  
24  25  C12  C11  C10  119.18  123.75  10000  1.98  -2.31  0.00  
25  25  C13  C12  C11  112.14  119.25  10000  1.48  -4.81  0.02  
26  25  C13  C14  C15  122.77  118.96   4982  1.27   3.01  0.01  
27  25  C14  C15  N4   116.44  121.23     79  0.85  -5.63  1.73  
28  25  C14  C15  N5   121.86  117.63   2755  1.34   3.17  0.04  
29  25  C19  C20  N6   125.77  122.04   3637  1.68   2.21  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   0.877  0.166   0.239  
 2   2  22   0.808  0.191   0.819  
 3   3  20   0.938  0.176   0.288  
 4   4  21   0.911  0.171   0.283  
 5   5  19   0.891  0.207   0.931  
 6   6  22   0.952  0.147  -0.011  
 7   7  16   0.827  0.309   2.651  
 8   8  22   0.917  0.172   0.460  
 9   9  20   0.911  0.244   1.334  
10  10  21   0.879  0.217   1.009  
11  11  19   0.897  0.185   0.560  
12  12  22   0.905  0.165   0.328  
13  13  19   0.905  0.174   0.498  
14  14  20   0.835  0.214   0.872  
15  15  21   0.920  0.194   0.646  
16  16  19   0.883  0.197   0.762  
17  17  22   0.840  0.231   1.574  
18  18  19   0.871  0.157   0.177  
19  19  20   0.923  0.175   0.272  
20  20  21   0.869  0.230   1.215  
21  21  19   0.838  0.262   1.858  
22  22  22   0.885  0.179   0.592  
23  23   1   0.922  0.105       ?  
24  24  27   0.960  0.207       ?  
25  25  27   0.965  0.209       ?  
26  26   1   0.949  0.346       ?  
27  27   1   0.829  0.500       ?  
28  28   1   0.865  0.406       ?  
29  29   1   0.633  0.479       ?  
30  30   1   0.790  0.499       ?  
31  31   1  -0.100  0.588       ?  
32  32   1   0.759  0.492       ?  
33  33   1   0.727  0.373       ?  
34  34   1   0.722  0.525       ?  
#
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                                                                  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  
##
