data_346D

_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  346D
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    346D
_pdbx_vrpt_summary.PDB_deposition_date         1997-08-26
_pdbx_vrpt_summary.PDB_revision_number         4
_pdbx_vrpt_summary.PDB_revision_date           2024-02-21
_pdbx_vrpt_summary.report_creation_date        2024-02-11:06:17
_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  "DNA (5'-D(*GP*(5CM)P*GP*(5CM)P*GP*(5CM)P*GP*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  2.1  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   66.84  141614     ?     ?  
2  2  1   67.99    5710  2.10  2.10  
3  1  2  100.00  127900     ?     ?  
4  2  2  100.00    5083  2.10  2.10  
#
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      0.73
_pdbx_vrpt_summary_entity_geometry.bonds_RMSZ       0.50
_pdbx_vrpt_summary_entity_geometry.num_bonds_RMSZ   114
_pdbx_vrpt_summary_entity_geometry.num_angles_RMSZ  168
#
_pdbx_vrpt_summary_geometry.ordinal          1
_pdbx_vrpt_summary_geometry.clashscore       3.85
_pdbx_vrpt_summary_geometry.num_H_reduce     96
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ   114
_pdbx_vrpt_summary_geometry.bonds_RMSZ       0.50
_pdbx_vrpt_summary_geometry.num_angles_RMSZ  168
_pdbx_vrpt_summary_geometry.angles_RMSZ      0.73
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            75.759
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         28.170
_pdbx_vrpt_summary_diffraction.I_over_sigma              0.57(1.85A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        2140
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.366
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.460
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.292
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.960
_pdbx_vrpt_summary_diffraction.DCC_R                     0.20
_pdbx_vrpt_summary_diffraction.EDS_R                     0.22
_pdbx_vrpt_summary_diffraction.EDS_res_high              1.85
_pdbx_vrpt_summary_diffraction.EDS_res_low               12.06
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[29.340,29.340,26.355,0.000,0.000,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.105
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The largest off-origin peak in the Patterson function is 13.42% 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         1
_pdbx_vrpt_summary_diffraction.centric_outliers          0
_pdbx_vrpt_summary_diffraction.data_completeness         88.31
_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       2.10
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        8.00
_pdbx_vrpt_summary_diffraction.PDB_R                     0.20
#
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_angle_outliers
 1  1  1  A  1  DG   A   1  .  ?        ?     ?  
 2  1  1  A  2  5CM  A   2  .  ?        ?     1  
 3  1  1  A  3  DG   A   3  .  ?        ?     ?  
 4  1  1  A  4  5CM  A   4  .  ?        2     1  
 5  1  1  A  5  DG   A   5  .  ?        ?     ?  
 6  1  1  A  6  5CM  A   6  .  ?        ?     1  
 7  1  1  A  7  DG   A   7  .  ?        ?     ?  
 8  1  1  A  8  DC   A   8  .  ?        ?     ?  
 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  .  ?        ?     ?  
#
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  21.640    21  0.57    31  0.45  molprobity  1.000  
 2   2    13  23.190    17  0.41    24  0.66  mogul       1.000  
 3   3    11  22.750    24  0.57    35  0.88  molprobity  1.000  
 4   4    13  20.570    17  0.43    24  0.60  mogul       1.000  
 5   5    11  16.290    24  0.46    35  0.54  molprobity  1.000  
 6   6    13  15.910    17  0.48    24  0.72  mogul       1.000  
 7   7    11  18.010    25  0.54    39  0.72  molprobity  1.000  
 8   8    12  27.720    20  0.29    28  0.97  molprobity  1.000  
 9   9     ?  35.060     ?     ?     ?     ?  ?           1.000  
10  10     ?  38.630     ?     ?     ?     ?  ?           1.000  
11  11     ?  33.560     ?     ?     ?     ?  ?           1.000  
12  12     ?  37.250     ?     ?     ?     ?  ?           1.000  
13  13     ?  45.160     ?     ?     ?     ?  ?           1.000  
14  14     ?  37.050     ?     ?     ?     ?  ?           1.000  
15  15     ?  54.980     ?     ?     ?     ?  ?           0.500  
16  16     ?  44.070     ?     ?     ?     ?  ?           0.500  
17  17     ?  41.880     ?     ?     ?     ?  ?           1.000  
18  18     ?  64.460     ?     ?     ?     ?  ?           1.000  
19  19     ?  29.040     ?     ?     ?     ?  ?           1.000  
20  20     ?  37.610     ?     ?     ?     ?  ?           1.000  
21  21     ?  29.490     ?     ?     ?     ?  ?           1.000  
22  22     ?  23.510     ?     ?     ?     ?  ?           1.000  
23  23     ?  44.730     ?     ?     ?     ?  ?           1.000  
24  24     ?  64.930     ?     ?     ?     ?  ?           1.000  
25  25     ?  71.730     ?     ?     ?     ?  ?           1.000  
26  26     ?  42.150     ?     ?     ?     ?  ?           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  4  "O5'"  1  0.44  2.18  
2  4  H6     1  0.44  2.18  
#
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  2  C5  C6  N1  120.91  123.34  431  1.03  -2.36  0.05  
2  4  C5  C6  N1  121.04  123.34  431  1.03  -2.23  0.01  
3  6  C5  C6  N1  120.83  123.34  431  1.03  -2.44  0.13  
#
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  0.915  0.137   0.035  
 2   2  20  0.950  0.093       ?  
 3   3  22  0.933  0.105  -0.532  
 4   4  20  0.937  0.115       ?  
 5   5  22  0.947  0.096  -0.691  
 6   6  20  0.936  0.103       ?  
 7   7  22  0.949  0.092  -0.762  
 8   8  19  0.936  0.119  -0.330  
 9   9   1  0.876  0.224       ?  
10  10   1  0.771  0.301       ?  
11  11   1  0.924  0.163       ?  
12  12   1  0.651  0.189       ?  
13  13   1  0.794  0.360       ?  
14  14   1  0.982  0.110       ?  
15  15   1  0.786  0.109       ?  
16  16   1  0.045  1.050       ?  
17  17   1  0.745  0.207       ?  
18  18   1  0.828  0.340       ?  
19  19   1  0.722  0.176       ?  
20  20   1  0.756  0.171       ?  
21  21   1  0.685  0.334       ?  
22  22   1  0.937  0.084       ?  
23  23   1  0.602  0.404       ?  
24  24   1  0.662  0.577       ?  
25  25   1  0.629  0.552       ?  
26  26   1  0.954  0.238       ?  
#
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  
##
