data_1D79

_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  1D79
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    1D79
_pdbx_vrpt_summary.PDB_deposition_date         1992-06-12
_pdbx_vrpt_summary.PDB_revision_number         4
_pdbx_vrpt_summary.PDB_revision_date           2023-03-22
_pdbx_vrpt_summary.report_creation_date        2023-03-13:18:07
_pdbx_vrpt_summary.attempted_validation_steps  molprobity,validation-pack,xtriage,eds,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  "DNA (5'-D(*GP*TP*GP*TP*AP*CP*AP*C)-3')"  
2  water    water  
#
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  1.45  x-ray  
#
loop_
_pdbx_vrpt_percentile_type.id
_pdbx_vrpt_percentile_type.type
1  all_atom_clashscore    
2  RSRZ_outliers_percent  
#
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   21.54  141614     ?     ?  
2  2  1    5.74    1202  1.46  1.46  
3  1  2  100.00  127900     ?     ?  
4  2  2  100.00    1139  1.46  1.46  
#
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      2.71
_pdbx_vrpt_summary_entity_geometry.bonds_RMSZ       1.94
_pdbx_vrpt_summary_entity_geometry.num_bonds_RMSZ   180
_pdbx_vrpt_summary_entity_geometry.num_angles_RMSZ  276
#
_pdbx_vrpt_summary_geometry.ordinal          1
_pdbx_vrpt_summary_geometry.clashscore       11.86
_pdbx_vrpt_summary_geometry.num_H_reduce     92
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ   180
_pdbx_vrpt_summary_geometry.bonds_RMSZ       1.94
_pdbx_vrpt_summary_geometry.num_angles_RMSZ  276
_pdbx_vrpt_summary_geometry.angles_RMSZ      2.71
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.Babinet_b                 214.988
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            145.886
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         14.398
_pdbx_vrpt_summary_diffraction.I_over_sigma              1.91(1.46A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        6419
_pdbx_vrpt_summary_diffraction.Babinet_k                 0.672
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            1.050
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.482
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.317
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.972
_pdbx_vrpt_summary_diffraction.DCC_R                     0.19
_pdbx_vrpt_summary_diffraction.EDS_R                     0.19
_pdbx_vrpt_summary_diffraction.EDS_res_high              1.46
_pdbx_vrpt_summary_diffraction.EDS_res_low               28.01
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[13.499,13.499,21.204,0.000,0.000,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.480
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The largest off-origin peak in the Patterson function is 14.85% 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         73.96
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      0
_pdbx_vrpt_summary_diffraction.percent_free_reflections  0.00
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     0.00
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       1.45
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        5.00
_pdbx_vrpt_summary_diffraction.PDB_R                     0.19
#
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  1  1  A  2  DT   A   2  .  ?        ?     5     ?  
 3  1  1  A  3  DG   A   3  .  ?        2     3     ?  
 4  1  1  A  4  DT   A   4  .  ?        1     2     ?  
 5  1  1  A  5  DA   A   5  .  ?        ?     4     ?  
 6  1  1  A  6  DC   A   6  .  ?        1     2     3  
 7  1  1  A  7  DA   A   7  .  ?        ?     5     ?  
 8  1  1  A  8  DC   A   8  .  ?        1     1     ?  
 9  1  2  B  .  HOH  A   9  .  ?        ?     ?     ?  
10  1  2  B  .  HOH  A  10  .  ?        ?     ?     ?  
11  1  2  B  .  HOH  A  11  .  ?        ?     ?     ?  
12  1  2  B  .  HOH  A  12  .  ?        ?     ?     ?  
13  1  2  B  .  HOH  A  13  .  ?        ?     ?     ?  
14  1  2  B  .  HOH  A  14  .  ?        ?     ?     ?  
15  1  2  B  .  HOH  A  15  .  ?        ?     ?     ?  
16  1  2  B  .  HOH  A  16  .  ?        ?     ?     ?  
17  1  2  B  .  HOH  A  17  .  ?        ?     ?     ?  
18  1  2  B  .  HOH  A  18  .  ?        ?     ?     ?  
19  1  2  B  .  HOH  A  19  .  ?        ?     ?     ?  
20  1  2  B  .  HOH  A  20  .  ?        ?     ?     ?  
21  1  2  B  .  HOH  A  21  .  ?        ?     ?     ?  
22  1  2  B  .  HOH  A  22  .  ?        ?     ?     ?  
23  1  2  B  .  HOH  A  23  .  ?        ?     ?     ?  
24  1  2  B  .  HOH  A  24  .  ?        ?     ?     ?  
25  1  2  B  .  HOH  A  25  .  ?        ?     ?     ?  
26  1  2  B  .  HOH  A  26  .  ?        ?     ?     ?  
27  1  2  B  .  HOH  A  27  .  ?        ?     ?     ?  
28  1  2  B  .  HOH  A  28  .  ?        ?     ?     ?  
29  1  2  B  .  HOH  A  29  .  ?        ?     ?     ?  
30  1  2  B  .  HOH  A  30  .  ?        ?     ?     ?  
31  1  2  B  .  HOH  A  31  .  ?        ?     ?     ?  
32  1  2  B  .  HOH  A  32  .  ?        ?     ?     ?  
33  1  2  B  .  HOH  A  33  .  ?        ?     ?     ?  
34  1  2  B  .  HOH  A  34  .  ?        ?     ?     ?  
35  1  2  B  .  HOH  A  35  .  ?        ?     ?     ?  
36  1  2  B  .  HOH  A  36  .  ?        ?     ?     ?  
37  1  2  B  .  HOH  A  37  .  ?        ?     ?     ?  
38  1  2  B  .  HOH  A  38  .  ?        ?     ?     ?  
39  1  2  B  .  HOH  A  39  .  ?        ?     ?     ?  
40  1  2  B  .  HOH  A  40  .  ?        ?     ?     3  
41  1  2  B  .  HOH  A  41  .  ?        ?     ?     ?  
42  1  2  B  .  HOH  A  42  .  ?        ?     ?     ?  
43  1  2  B  .  HOH  A  43  .  ?        ?     ?     ?  
#
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  15.880    22  1.41    35  1.79  molprobity  1.000  
 2   2    12  16.570    22  2.02    34  3.31  molprobity  1.000  
 3   3    11  16.840    25  2.28    39  2.66  molprobity  1.000  
 4   4    12  17.260    22  2.30    34  2.63  molprobity  1.000  
 5   5    11  17.710    24  1.60    37  3.24  molprobity  1.000  
 6   6    11  16.310    21  2.04    32  2.51  molprobity  1.000  
 7   7    11  17.650    24  1.40    37  2.68  molprobity  1.000  
 8   8    12  22.620    20  2.29    28  2.54  molprobity  1.000  
 9   9     ?  34.850     ?     ?     ?     ?  ?           0.960  
10  10     ?  44.320     ?     ?     ?     ?  ?           1.000  
11  11     ?  32.750     ?     ?     ?     ?  ?           0.990  
12  12     ?  55.360     ?     ?     ?     ?  ?           0.820  
13  13     ?  27.440     ?     ?     ?     ?  ?           0.950  
14  14     ?  27.970     ?     ?     ?     ?  ?           0.960  
15  15     ?  26.620     ?     ?     ?     ?  ?           1.000  
16  16     ?  26.380     ?     ?     ?     ?  ?           0.970  
17  17     ?  50.610     ?     ?     ?     ?  ?           0.940  
18  18     ?  41.910     ?     ?     ?     ?  ?           0.920  
19  19     ?  51.760     ?     ?     ?     ?  ?           1.000  
20  20     ?  49.380     ?     ?     ?     ?  ?           0.940  
21  21     ?  26.580     ?     ?     ?     ?  ?           1.000  
22  22     ?  36.560     ?     ?     ?     ?  ?           0.850  
23  23     ?  53.870     ?     ?     ?     ?  ?           0.960  
24  24     ?  30.260     ?     ?     ?     ?  ?           0.960  
25  25     ?  32.420     ?     ?     ?     ?  ?           1.000  
26  26     ?  37.960     ?     ?     ?     ?  ?           1.000  
27  27     ?  26.140     ?     ?     ?     ?  ?           0.940  
28  28     ?  38.730     ?     ?     ?     ?  ?           0.850  
29  29     ?  46.790     ?     ?     ?     ?  ?           0.910  
30  30     ?  29.110     ?     ?     ?     ?  ?           0.890  
31  31     ?  51.070     ?     ?     ?     ?  ?           0.680  
32  32     ?  36.980     ?     ?     ?     ?  ?           0.870  
33  33     ?  52.650     ?     ?     ?     ?  ?           1.000  
34  34     ?  28.230     ?     ?     ?     ?  ?           0.970  
35  35     ?  34.910     ?     ?     ?     ?  ?           0.930  
36  36     ?  49.210     ?     ?     ?     ?  ?           0.730  
37  37     ?  32.320     ?     ?     ?     ?  ?           0.860  
38  38     ?  40.700     ?     ?     ?     ?  ?           0.930  
39  39     ?  57.930     ?     ?     ?     ?  ?           0.900  
40  40     ?  52.460     ?     ?     ?     ?  ?           0.590  
41  41     ?  54.440     ?     ?     ?     ?  ?           0.740  
42  42     ?  35.290     ?     ?     ?     ?  ?           0.960  
43  43     ?  62.700     ?     ?     ?     ?  ?           0.950  
#
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  C5  1  0.84  2.31  
2   6  C6  2  0.67  2.46  
3   6  H5  3  0.57  1.75  
4  40  O   1  0.84  2.31  
5  40  O   2  0.67  2.46  
6  40  O   3  0.57  1.75  
#
loop_
_pdbx_vrpt_instance_intra_bond_outliers.ordinal
_pdbx_vrpt_instance_intra_bond_outliers.instance_id
_pdbx_vrpt_instance_intra_bond_outliers.atom_1
_pdbx_vrpt_instance_intra_bond_outliers.atom_2
_pdbx_vrpt_instance_intra_bond_outliers.obs
_pdbx_vrpt_instance_intra_bond_outliers.mean
_pdbx_vrpt_instance_intra_bond_outliers.stdev
_pdbx_vrpt_instance_intra_bond_outliers.Z
_pdbx_vrpt_instance_intra_bond_outliers.link
1  3  "O3'"  P      1.517  1.607  0.012  -7.49  Y     
2  3  P      "O5'"  1.660  1.593  0.010   6.73  ?     
3  4  P      "O5'"  1.661  1.593  0.010   6.83  ?     
4  6  P      OP1    1.583  1.485  0.017   5.76  ?     
5  8  P      "O5'"  1.667  1.593  0.010   7.42  ?     
#
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
_pdbx_vrpt_instance_intra_angle_outliers.link
 1  2  OP2    P      "O3'"  121.208  105.200  2.200    7.28  Y     
 2  2  C2     N3     C4     123.029  127.200  0.600   -6.95  ?     
 3  2  C5     C4     O4     121.008  124.900  0.700   -5.56  ?     
 4  2  N3     C4     C5     120.368  115.200  0.600    8.61  ?     
 5  2  "O5'"  P      OP2    118.071  110.700  1.200    6.14  ?     
 6  3  OP2    P      "O3'"  117.593  105.200  2.200    5.63  Y     
 7  3  P      "O3'"  "C3'"  126.525  119.700  1.200    5.69  Y     
 8  3  "O5'"  P      OP2     98.314  105.700  0.900   -8.21  ?     
 9  4  C2     N3     C4     122.715  127.200  0.600   -7.48  ?     
10  4  N3     C4     C5     118.765  115.200  0.600    5.94  ?     
11  5  C2     N3     C4     114.019  110.600  0.500    6.84  ?     
12  5  C6     N1     C2     122.834  118.600  0.600    7.06  ?     
13  5  N1     C2     N3     123.393  129.300  0.500  -11.81  ?     
14  5  OP1    P      OP2    110.142  119.600  1.500   -6.31  ?     
15  6  P      "O3'"  "C3'"  126.226  119.700  1.200    5.44  Y     
16  6  N3     C4     C5     119.263  121.900  0.400   -6.59  ?     
17  7  C5     C6     N1     114.091  117.700  0.500   -7.22  ?     
18  7  C6     N1     C2     122.655  118.600  0.600    6.76  ?     
19  7  N1     C2     N3     125.511  129.300  0.500   -7.58  ?     
20  7  N1     C6     N6     121.901  118.600  0.600    5.50  ?     
21  7  OP1    P      OP2    112.025  119.600  1.500   -5.05  ?     
22  8  N3     C4     C5     119.395  121.900  0.400   -6.26  ?     
#
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  0.960  0.152  1.056  
 2   2  20  0.964  0.130  0.310  
 3   3  22  0.954  0.127  0.573  
 4   4  20  0.959  0.151  0.636  
 5   5  21  0.959  0.162  0.855  
 6   6  19  0.967  0.160  0.890  
 7   7  21  0.954  0.158  0.797  
 8   8  19  0.923  0.153  0.777  
 9   9   1  0.819  0.279      ?  
10  10   1  0.894  0.308      ?  
11  11   1  0.934  0.254      ?  
12  12   1  0.599  0.547      ?  
13  13   1  0.946  0.156      ?  
14  14   1  0.933  0.197      ?  
15  15   1  0.943  0.158      ?  
16  16   1  0.944  0.189      ?  
17  17   1  0.783  0.370      ?  
18  18   1  0.891  0.305      ?  
19  19   1  0.748  0.850      ?  
20  20   1  0.613  0.284      ?  
21  21   1  0.958  0.158      ?  
22  22   1  0.700  0.305      ?  
23  23   1  0.821  0.714      ?  
24  24   1  0.907  0.204      ?  
25  25   1  0.867  0.276      ?  
26  26   1  0.955  0.558      ?  
27  27   1  0.966  0.272      ?  
28  28   1  0.830  0.390      ?  
29  29   1  0.591  0.357      ?  
30  30   1  0.895  0.288      ?  
31  31   1  0.953  0.718      ?  
32  32   1  0.893  0.212      ?  
33  33   1  0.573  0.406      ?  
34  34   1  0.951  0.137      ?  
35  35   1  0.806  0.241      ?  
36  36   1  0.836  0.201      ?  
37  37   1  0.873  0.248      ?  
38  38   1  0.683  0.267      ?  
39  39   1  0.360  0.446      ?  
40  40   1  0.727  1.323      ?  
41  41   1  0.406  0.540      ?  
42  42   1  0.845  0.207      ?  
43  43   1  0.550  0.565      ?  
#
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          2.32.1                                                                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  
##
