data_8D79

_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  8D79
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    8D79
_pdbx_vrpt_summary.PDB_deposition_date         2022-06-07
_pdbx_vrpt_summary.PDB_revision_number         2
_pdbx_vrpt_summary.PDB_revision_date           2023-10-25
_pdbx_vrpt_summary.report_creation_date        2023-10-15:01:29
_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(*TP*GP*GP*GP*GP*TP*TP*GP*GP*GP*GP*TP*TP*GP*GP*GP*GP*TP*TP*GP*GP*GP*GP*T)-3')"  
2  non-polymer  "SODIUM ION"  
3  non-polymer  N-METHYLMESOPORPHYRIN  
4  non-polymer  (4S)-2-METHYL-2,4-PENTANEDIOL  
5  water        water  
#
loop_
_pdbx_vrpt_asym.label_asym_id
_pdbx_vrpt_asym.entity_id
A  1  
B  2  
C  2  
D  2  
E  2  
F  2  
G  3  
H  4  
I  4  
J  5  
#
loop_
_pdbx_vrpt_percentile_list.id
_pdbx_vrpt_percentile_list.range
_pdbx_vrpt_percentile_list.exp_method
1  all   x-ray  
2  1.99  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  23.76  141614     ?     ?  
2  2  1  20.23    9178  2.00  2.00  
3  1  2   1.03  127900     ?     ?  
4  2  2   0.80    7900  2.00  2.00  
5  1  3  27.11  130704     ?     ?  
6  2  3  20.49    8085  2.00  2.00  
#
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  1.03  
2  4  2  A  1  1  A  0.80  
#
_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      0.92
_pdbx_vrpt_summary_entity_geometry.bonds_RMSZ       0.56
_pdbx_vrpt_summary_entity_geometry.num_bonds_RMSZ   525
_pdbx_vrpt_summary_entity_geometry.num_angles_RMSZ  815
#
_pdbx_vrpt_summary_geometry.ordinal          1
_pdbx_vrpt_summary_geometry.clashscore       11.11
_pdbx_vrpt_summary_geometry.num_H_reduce     289
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ   525
_pdbx_vrpt_summary_geometry.bonds_RMSZ       0.56
_pdbx_vrpt_summary_geometry.num_angles_RMSZ  815
_pdbx_vrpt_summary_geometry.angles_RMSZ      0.92
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.Babinet_b                 82.068
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            58.678
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         56.995
_pdbx_vrpt_summary_diffraction.I_over_sigma              0.99(1.98A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        3899
_pdbx_vrpt_summary_diffraction.Babinet_k                 0.675
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.284
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.527
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.367
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.956
_pdbx_vrpt_summary_diffraction.DCC_R                     0.25
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.26
_pdbx_vrpt_summary_diffraction.EDS_R                     0.26
_pdbx_vrpt_summary_diffraction.EDS_res_high              1.99
_pdbx_vrpt_summary_diffraction.EDS_res_low               32.97
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[59.484,68.304,35.957,0.000,4.877,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.593
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The largest off-origin peak in the Patterson function is 17.40% 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         18
_pdbx_vrpt_summary_diffraction.centric_outliers          1
_pdbx_vrpt_summary_diffraction.data_completeness         96.92
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      180
_pdbx_vrpt_summary_diffraction.percent_free_reflections  4.62
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     17.39
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       1.99
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        32.97
_pdbx_vrpt_summary_diffraction.PDB_R                     0.24
_pdbx_vrpt_summary_diffraction.PDB_Rfree                 0.25
#
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.count_mogul_torsion_outliers
 1  1  1  A   2  DG   A    2  .  ?        ?     ?     ?     ?  
 2  1  1  A   3  DG   A    3  .  ?        ?     ?     ?     ?  
 3  1  1  A   4  DG   A    4  .  ?        ?     ?     ?     ?  
 4  1  1  A   5  DG   A    5  .  ?        ?     ?     ?     ?  
 5  1  1  A   6  DT   A    6  .  ?        ?     ?     ?     ?  
 6  1  1  A   7  DT   A    7  .  ?        ?     ?     ?     ?  
 7  1  1  A   8  DG   A    8  .  ?        1     ?     ?     ?  
 8  1  1  A   9  DG   A    9  .  ?        ?     ?     ?     ?  
 9  1  1  A  10  DG   A   10  .  ?        ?     ?     ?     ?  
10  1  1  A  11  DG   A   11  .  ?        1     ?     ?     ?  
11  1  1  A  12  DT   A   12  .  ?        ?     ?     ?     ?  
12  1  1  A  13  DT   A   13  .  ?        ?     ?     ?     ?  
13  1  1  A  14  DG   A   14  .  ?        ?     ?     ?     ?  
14  1  1  A  15  DG   A   15  .  ?        ?     ?     ?     ?  
15  1  1  A  16  DG   A   16  .  ?        ?     ?     ?     ?  
16  1  1  A  17  DG   A   17  .  ?        ?     ?     ?     ?  
17  1  1  A  18  DT   A   18  .  ?        ?     ?     ?     ?  
18  1  1  A  19  DT   A   19  .  ?        ?     ?     ?     ?  
19  1  1  A  20  DG   A   20  .  ?        1     ?     ?     ?  
20  1  1  A  21  DG   A   21  .  ?        ?     ?     ?     ?  
21  1  1  A  22  DG   A   22  .  ?        ?     ?     ?     ?  
22  1  1  A  23  DG   A   23  .  ?        ?     ?     ?     ?  
23  1  1  A  24  DT   A   24  .  ?        ?     ?     ?     ?  
24  1  2  B   .  NA   A  101  .  ?        ?     ?     ?     ?  
25  1  2  C   .  NA   A  102  .  ?        ?     ?     ?     ?  
26  1  2  D   .  NA   A  103  .  ?        ?     ?     ?     ?  
27  1  2  E   .  NA   A  104  .  ?        ?     ?     ?     ?  
28  1  2  F   .  NA   A  105  .  ?        ?     ?     ?     ?  
29  1  3  G   .  MMP  A  106  .  ?       11     5     9     ?  
30  1  4  H   .  MPD  A  107  .  ?        3     ?     ?     1  
31  1  4  I   .  MPD  A  108  .  ?        1     ?     ?     2  
32  1  5  J   .  HOH  A  201  .  ?        ?     ?     ?     ?  
33  1  5  J   .  HOH  A  202  .  ?        ?     ?     ?     ?  
34  1  5  J   .  HOH  A  203  .  ?        ?     ?     ?     ?  
35  1  5  J   .  HOH  A  204  .  ?        ?     ?     ?     ?  
36  1  5  J   .  HOH  A  205  .  ?        ?     ?     ?     ?  
37  1  5  J   .  HOH  A  206  .  ?        ?     ?     ?     ?  
38  1  5  J   .  HOH  A  207  .  ?        ?     ?     ?     ?  
39  1  5  J   .  HOH  A  208  .  ?        ?     ?     ?     ?  
40  1  5  J   .  HOH  A  209  .  ?        ?     ?     ?     ?  
41  1  5  J   .  HOH  A  210  .  ?        ?     ?     ?     ?  
42  1  5  J   .  HOH  A  211  .  ?        ?     ?     ?     ?  
43  1  5  J   .  HOH  A  212  .  ?        ?     ?     ?     ?  
#
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    11   66.850    25  0.42    39  0.79  molprobity  1.000  
 2   2    11   63.190    25  0.52    39  0.78  molprobity  1.000  
 3   3    11   64.870    25  0.62    39  0.85  molprobity  1.000  
 4   4    11   67.710    25  0.52    39  0.85  molprobity  1.000  
 5   5    12   92.700    22  0.55    34  1.26  molprobity  1.000  
 6   6    12   88.760    22  0.46    34  1.19  molprobity  1.000  
 7   7    11   62.530    25  0.43    39  0.77  molprobity  1.000  
 8   8    11   62.670    25  0.53    39  0.66  molprobity  1.000  
 9   9    11   68.910    25  0.49    39  0.70  molprobity  1.000  
10  10    11   75.710    25  0.40    39  0.75  molprobity  1.000  
11  11     6  120.260    12  0.47    18  0.85  molprobity  1.000  
12  12    12  117.170    22  0.57    34  1.31  molprobity  1.000  
13  13    11   71.060    25  0.46    39  0.85  molprobity  1.000  
14  14    11   69.290    25  0.59    39  0.74  molprobity  1.000  
15  15    11   68.100    25  0.69    39  0.79  molprobity  1.000  
16  16    11   74.810    25  0.69    39  0.95  molprobity  1.000  
17  17    12  107.970    22  0.58    34  1.24  molprobity  1.000  
18  18    12  107.240    22  0.82    34  1.38  molprobity  1.000  
19  19    11   72.690    25  0.65    39  0.70  molprobity  1.000  
20  20    11   64.320    25  0.51    39  0.78  molprobity  1.000  
21  21    11   63.100    25  0.58    39  0.73  molprobity  1.000  
22  22    11   68.340    25  0.48    39  0.97  molprobity  1.000  
23  23     ?   91.580     3  0.46     3  1.35  molprobity  1.000  
24  24     ?   47.990     ?     ?     ?     ?  ?           1.000  
25  25     ?   50.420     ?     ?     ?     ?  ?           1.000  
26  26     ?   54.680     ?     ?     ?     ?  ?           1.000  
27  27     ?   46.990     ?     ?     ?     ?  ?           0.500  
28  28     ?   98.490     ?     ?     ?     ?  ?           0.500  
29  29    20   73.660    19  6.20    17  5.35  mogul       1.000  
30  30    13  141.190     7  0.73     9  0.55  mogul       0.500  
31  31    14   88.310     7  0.70     9  0.32  mogul       0.500  
32  32     ?   76.720     ?     ?     ?     ?  ?           1.000  
33  33     ?   74.170     ?     ?     ?     ?  ?           1.000  
34  34     ?   94.150     ?     ?     ?     ?  ?           1.000  
35  35     ?   87.560     ?     ?     ?     ?  ?           1.000  
36  36     ?   68.060     ?     ?     ?     ?  ?           1.000  
37  37     ?   66.980     ?     ?     ?     ?  ?           1.000  
38  38     ?   71.940     ?     ?     ?     ?  ?           1.000  
39  39     ?   94.360     ?     ?     ?     ?  ?           1.000  
40  40     ?   94.580     ?     ?     ?     ?  ?           1.000  
41  41     ?  106.080     ?     ?     ?     ?  ?           1.000  
42  42     ?   64.990     ?     ?     ?     ?  ?           1.000  
43  43     ?   85.980     ?     ?     ?     ?  ?           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   7  "H4'"  1  0.51  1.92  
 2  10  C6     2  0.54  2.43  
 3  19  P      3  0.53  2.49  
 4  29  C44    4  1.21  1.94  
 5  29  N4     4  1.21  1.94  
 6  29  N4     5  0.65  2.11  
 7  29  N2     6  1.16  1.95  
 8  29  N2     7  0.41  2.84  
 9  29  N2     8  0.41  2.36  
10  29  C24    6  1.16  1.95  
11  29  H12    5  0.65  2.11  
12  29  H13    2  0.54  2.43  
13  29  C1     7  0.41  2.84  
14  29  H11    8  0.41  2.36  
15  30  HM3    3  0.53  2.49  
16  30  HM2    9  0.43  1.75  
17  30  H4     9  0.43  1.75  
18  31  H12    1  0.51  1.92  
#
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  29  C1   N1  1.45  1.48  148  0.01  -2.64  0.01  
2  29  C21  N2  1.49  1.37   27  0.03   3.90  0.08  
3  29  C24  N2  1.95  1.37   27  0.03  18.56  0.54  
4  29  C41  N4  1.47  1.37   27  0.03   3.21  0.06  
5  29  C44  N4  1.94  1.37   27  0.03  18.39  0.53  
#
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  29  C21  C22  C23  118.19  108.61   20  0.83  11.52  7.83  
2  29  C26  C22  C23  120.09  126.75  795  2.08  -3.20  0.33  
3  29  C24  C23  C22  117.30  108.61   20  0.83  10.45  6.94  
4  29  C27  C23  C22  120.79  126.75  795  2.08  -2.87  0.37  
5  29  C41  C42  C43  118.60  108.61   20  0.83  12.01  8.24  
6  29  C47  C42  C41  120.44  124.73  906  1.89  -2.27  0.04  
7  29  C47  C42  C43  120.97  126.75  795  2.08  -2.78  0.33  
8  29  C44  C43  C42  114.92  108.61   20  0.83   7.59  4.56  
9  29  C46  C43  C42  122.44  126.75  795  2.08  -2.07  0.04  
#
loop_
_pdbx_vrpt_instance_mogul_torsion_outliers.ordinal
_pdbx_vrpt_instance_mogul_torsion_outliers.instance_id
_pdbx_vrpt_instance_mogul_torsion_outliers.atom_1
_pdbx_vrpt_instance_mogul_torsion_outliers.atom_2
_pdbx_vrpt_instance_mogul_torsion_outliers.atom_3
_pdbx_vrpt_instance_mogul_torsion_outliers.atom_4
_pdbx_vrpt_instance_mogul_torsion_outliers.obsval
_pdbx_vrpt_instance_mogul_torsion_outliers.mean
_pdbx_vrpt_instance_mogul_torsion_outliers.numobs
_pdbx_vrpt_instance_mogul_torsion_outliers.stdev
_pdbx_vrpt_instance_mogul_torsion_outliers.mindiff
_pdbx_vrpt_instance_mogul_torsion_outliers.local_density
1  30  C2  C3  C4  C5  -116.65  48.42  44  12.20  6.91  2.27  
2  31  C2  C3  C4  O4   109.84  46.35  41  19.56  5.28  4.88  
3  31  C2  C3  C4  C5  -130.26  39.14  44  13.30  2.69  4.55  
#
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  22   0.824  0.176  0.864  
 2   2  22   0.891  0.136  0.190  
 3   3  22   0.881  0.150  0.426  
 4   4  22   0.904  0.147  0.375  
 5   5  20   0.874  0.253  1.849  
 6   6  20   0.745  0.227  1.460  
 7   7  22   0.877  0.172  0.796  
 8   8  22   0.877  0.141  0.274  
 9   9  22   0.859  0.162  0.628  
10  10  22   0.920  0.165  0.678  
11  11  11   0.793  0.474  5.152  
12  12  20   0.380  0.503  5.586  
13  13  22   0.843  0.211  1.453  
14  14  22   0.855  0.189  1.082  
15  15  22   0.868  0.152  0.460  
16  16  22   0.886  0.169  0.746  
17  17  20   0.785  0.357  3.404  
18  18  20   0.779  0.294  2.462  
19  19  22   0.898  0.166  0.695  
20  20  22   0.882  0.183  0.981  
21  21  22   0.891  0.162  0.628  
22  22  22   0.911  0.159  0.577  
23  23   4   0.871  0.135  0.085  
24  24   1   0.842  0.207      ?  
25  25   1   0.433  0.247      ?  
26  26   1   0.817  0.386      ?  
27  27   1   0.896  0.191      ?  
28  28   1   0.517  0.390      ?  
29  29  33   0.798  0.290      ?  
30  30   8   0.127  0.888      ?  
31  31   8   0.801  0.298      ?  
32  32   1   0.753  0.492      ?  
33  33   1   0.171  0.504      ?  
34  34   1   0.450  0.773      ?  
35  35   1   0.721  0.498      ?  
36  36   1  -0.102  0.593      ?  
37  37   1   0.794  0.601      ?  
38  38   1   0.658  0.563      ?  
39  39   1   0.872  1.060      ?  
40  40   1   0.888  1.266      ?  
41  41   1   0.649  0.913      ?  
42  42   1   0.784  0.636      ?  
43  43   1   0.117  0.936      ?  
#
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        "1.8.5 (274361), 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  
##
