data_7Z82

_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  7Z82
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    7Z82
_pdbx_vrpt_summary.PDB_deposition_date         2022-03-16
_pdbx_vrpt_summary.PDB_revision_number         2
_pdbx_vrpt_summary.PDB_revision_date           2023-10-11
_pdbx_vrpt_summary.report_creation_date        2023-10-03:12:10
_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      "Chom18-AG DNA"  
2  non-polymer  "STRONTIUM ION"  
#
loop_
_pdbx_vrpt_asym.label_asym_id
_pdbx_vrpt_asym.entity_id
A  1  
B  2  
#
loop_
_pdbx_vrpt_percentile_list.id
_pdbx_vrpt_percentile_list.range
_pdbx_vrpt_percentile_list.exp_method
1  all  x-ray  
2  3.2  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   13.72  141614     ?     ?  
2  2  1   46.37    1253  3.20  3.20  
3  1  2  100.00  127900     ?     ?  
4  2  2  100.00    1095  3.20  3.20  
5  1  3    3.26  130704     ?     ?  
6  2  3   14.38    1133  3.20  3.20  
#
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  
#
_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      1.12
_pdbx_vrpt_summary_entity_geometry.bonds_RMSZ       0.99
_pdbx_vrpt_summary_entity_geometry.num_bonds_RMSZ   413
_pdbx_vrpt_summary_entity_geometry.num_angles_RMSZ  636
#
_pdbx_vrpt_summary_geometry.ordinal          1
_pdbx_vrpt_summary_geometry.clashscore       15.79
_pdbx_vrpt_summary_geometry.num_H_reduce     201
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ   413
_pdbx_vrpt_summary_geometry.bonds_RMSZ       0.99
_pdbx_vrpt_summary_geometry.num_angles_RMSZ  636
_pdbx_vrpt_summary_geometry.angles_RMSZ      1.12
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.Babinet_b                 54.623
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            87.501
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         101.921
_pdbx_vrpt_summary_diffraction.I_over_sigma              1.91(2.95A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        1535
_pdbx_vrpt_summary_diffraction.Babinet_k                 0.109
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.211
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.463
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.294
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.924
_pdbx_vrpt_summary_diffraction.DCC_R                     0.30
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.31
_pdbx_vrpt_summary_diffraction.EDS_R                     0.33
_pdbx_vrpt_summary_diffraction.EDS_res_high              2.95
_pdbx_vrpt_summary_diffraction.EDS_res_low               34.96
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[123.132,123.132,72.587,0.000,0.000,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.476
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The largest off-origin peak in the Patterson function is 7.47% 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         97.52
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      67
_pdbx_vrpt_summary_diffraction.percent_free_reflections  4.36
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     0.00
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       3.20
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        34.96
_pdbx_vrpt_summary_diffraction.PDB_R                     0.30
_pdbx_vrpt_summary_diffraction.PDB_Rfree                 0.32
#
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_bond_outliers
_pdbx_vrpt_model_instance.count_angle_outliers
_pdbx_vrpt_model_instance.count_clashes
 1  1  1  A   1  DG  A    1  .  ?        ?     ?     2  
 2  1  1  A   2  DG  A    2  .  ?        ?     ?     ?  
 3  1  1  A   3  DT  A    3  .  ?        ?     ?     ?  
 4  1  1  A   4  DG  A    4  .  ?        ?     1     2  
 5  1  1  A   5  DG  A    5  .  ?        ?     ?     2  
 6  1  1  A   6  DG  A    6  .  ?        ?     ?     ?  
 7  1  1  A   7  DG  A    7  .  ?        ?     ?     1  
 8  1  1  A   8  DC  A    8  .  ?        ?     1     1  
 9  1  1  A   9  DA  A    9  .  ?        ?     ?     1  
10  1  1  A  10  DG  A   10  .  ?        ?     ?     1  
11  1  1  A  11  DG  A   11  .  ?        ?     1     ?  
12  1  1  A  12  DC  A   12  .  ?        ?     ?     ?  
13  1  1  A  13  DC  A   13  .  ?        ?     ?     2  
14  1  1  A  14  DC  A   14  .  ?        ?     ?     2  
15  1  1  A  15  DC  A   15  .  ?        ?     ?     ?  
16  1  1  A  16  DA  A   16  .  ?        1     ?     2  
17  1  1  A  17  DC  A   17  .  ?        ?     ?     2  
18  1  1  A  18  DC  A   18  .  ?        ?     ?     ?  
19  1  2  B   .  SR  A  101  .  ?        ?     ?     ?  
#
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   91.530    22  0.82    35  0.84  molprobity  1.000  
 2   2    11  101.160    25  0.65    39  0.90  molprobity  1.000  
 3   3    12  100.440    22  0.97    34  1.42  molprobity  1.000  
 4   4    11   94.480    25  0.86    39  1.28  molprobity  1.000  
 5   5    11   98.410    25  0.65    39  1.03  molprobity  1.000  
 6   6    11  102.590    25  0.60    39  0.62  molprobity  1.000  
 7   7    11  123.870    25  0.56    39  0.83  molprobity  1.000  
 8   8    11  145.920    21  1.09    32  2.06  molprobity  1.000  
 9   9    11  162.600    24  1.56    37  1.21  molprobity  1.000  
10  10    11  156.080    25  0.90    39  1.00  molprobity  1.000  
11  11    11  152.760    25  0.82    39  1.67  molprobity  1.000  
12  12    11  148.860    21  1.02    32  0.75  molprobity  1.000  
13  13    11  134.140    21  0.84    32  0.79  molprobity  1.000  
14  14    11  118.310    21  0.62    32  0.94  molprobity  1.000  
15  15    11   99.390    21  1.02    32  0.75  molprobity  1.000  
16  16    11   84.080    24  2.06    37  0.89  molprobity  1.000  
17  17    11   96.340    21  0.82    32  1.19  molprobity  1.000  
18  18    12  107.530    20  0.66    28  0.96  molprobity  1.000  
19  19     ?  141.870     ?     ?     ?     ?  ?           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  "O5'"   1  0.44  1.99  
 2   1  H8      1  0.44  1.99  
 3   4  "H2'"   2  0.62  1.65  
 4   4  "H2'"   3  0.55  2.41  
 5   5  H8      2  0.62  1.65  
 6   5  C8      3  0.55  2.41  
 7   7  "H2'"   4  0.45  2.52  
 8   8  C6      4  0.45  2.52  
 9   9  "H2''"  5  0.46  2.50  
10  10  C8      5  0.46  2.50  
11  13  "H2'"   6  0.45  1.82  
12  13  "H2'"   7  0.43  2.53  
13  14  H6      6  0.45  1.82  
14  14  C6      7  0.43  2.53  
15  16  "H2'"   8  0.51  2.45  
16  16  "H2'"   9  0.47  1.79  
17  17  C6      8  0.51  2.45  
18  17  H6      9  0.47  1.79  
#
_pdbx_vrpt_instance_intra_bond_outliers.ordinal      1
_pdbx_vrpt_instance_intra_bond_outliers.instance_id  16
_pdbx_vrpt_instance_intra_bond_outliers.atom_1       "C3'"
_pdbx_vrpt_instance_intra_bond_outliers.atom_2       "O3'"
_pdbx_vrpt_instance_intra_bond_outliers.obs          1.333
_pdbx_vrpt_instance_intra_bond_outliers.mean         1.435
_pdbx_vrpt_instance_intra_bond_outliers.stdev        0.013
_pdbx_vrpt_instance_intra_bond_outliers.Z            -7.87
#
loop_
_pdbx_vrpt_instance_intra_angle_outliers.ordinal
_pdbx_vrpt_instance_intra_angle_outliers.instance_id
_pdbx_vrpt_instance_intra_angle_outliers.atom_1
_pdbx_vrpt_instance_intra_angle_outliers.atom_2
_pdbx_vrpt_instance_intra_angle_outliers.atom_3
_pdbx_vrpt_instance_intra_angle_outliers.obs
_pdbx_vrpt_instance_intra_angle_outliers.mean
_pdbx_vrpt_instance_intra_angle_outliers.stdev
_pdbx_vrpt_instance_intra_angle_outliers.Z
1   4  "O4'"  "C1'"  N9  111.846  108.000  0.700   5.49  
2   8  "O4'"  "C1'"  N1  113.988  108.000  0.700   8.55  
3  11  "O4'"  "C1'"  N9  103.384  108.000  0.700  -6.59  
#
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  19  0.932  0.186  -0.100  
 2   2  22  0.896  0.165  -0.361  
 3   3  20  0.886  0.167  -0.469  
 4   4  22  0.911  0.129  -0.807  
 5   5  22  0.929  0.188  -0.076  
 6   6  22  0.868  0.208   0.172  
 7   7  22  0.810  0.169  -0.311  
 8   8  19  0.850  0.228   0.294  
 9   9  21  0.732  0.171  -0.293  
10  10  22  0.683  0.161  -0.410  
11  11  22  0.804  0.123  -0.881  
12  12  19  0.744  0.142  -0.702  
13  13  19  0.870  0.115  -1.015  
14  14  19  0.887  0.138  -0.749  
15  15  19  0.901  0.150  -0.610  
16  16  21  0.886  0.177  -0.218  
17  17  19  0.911  0.293   1.048  
18  18  19  0.892  0.249   0.538  
19  19   1  0.873  0.082       ?  
#
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          2.35.1                                                                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  
##
