data_1R2O

loop_
_pdbx_vrpt_database.id
_pdbx_vrpt_database.code
PDB  1R2O    
NDB  UD0043  
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    1R2O
_pdbx_vrpt_summary.PDB_deposition_date         2003-09-29
_pdbx_vrpt_summary.PDB_revision_number         4
_pdbx_vrpt_summary.PDB_revision_date           2024-02-14
_pdbx_vrpt_summary.report_creation_date        2024-02-04:20:07
_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      "5'-D(*GP*CP*AP*TP*GP*CP*T)-3'"  
2  non-polymer  "NICKEL (II) ION"  
3  water        water  
#
loop_
_pdbx_vrpt_asym.label_asym_id
_pdbx_vrpt_asym.entity_id
A  1  
B  2  
C  3  
#
loop_
_pdbx_vrpt_percentile_list.id
_pdbx_vrpt_percentile_list.range
_pdbx_vrpt_percentile_list.exp_method
1  all   x-ray  
2  2.38  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   99.96  141614     ?     ?  
2  2  1  100.00    6082  2.36  2.40  
3  1  2    2.17  127900     ?     ?  
4  2  2    2.45    5397  2.36  2.40  
5  1  3   27.11  130704     ?     ?  
6  2  3   39.42    5509  2.36  2.40  
#
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  X  2.17  
2  4  2  A  1  1  X  2.45  
#
_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     X
_pdbx_vrpt_summary_entity_geometry.angles_RMSZ      2.10
_pdbx_vrpt_summary_entity_geometry.bonds_RMSZ       1.58
_pdbx_vrpt_summary_entity_geometry.num_bonds_RMSZ   177
_pdbx_vrpt_summary_entity_geometry.num_angles_RMSZ  269
#
_pdbx_vrpt_summary_geometry.ordinal          1
_pdbx_vrpt_summary_geometry.clashscore       0.00
_pdbx_vrpt_summary_geometry.num_H_reduce     94
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ   177
_pdbx_vrpt_summary_geometry.bonds_RMSZ       1.58
_pdbx_vrpt_summary_geometry.num_angles_RMSZ  269
_pdbx_vrpt_summary_geometry.angles_RMSZ      2.10
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.Babinet_b                 189.303
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            64.736
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         27.724
_pdbx_vrpt_summary_diffraction.I_over_sigma              17.71(2.38A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        849
_pdbx_vrpt_summary_diffraction.Babinet_k                 0.999
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.417
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.481
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.307
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.899
_pdbx_vrpt_summary_diffraction.DCC_R                     0.24
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.26
_pdbx_vrpt_summary_diffraction.EDS_R                     0.24
_pdbx_vrpt_summary_diffraction.EDS_res_high              2.39
_pdbx_vrpt_summary_diffraction.EDS_res_low               21.48
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[31.115,31.115,21.806,-0.000,0.000,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.332
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The analyses of the Patterson function reveals a significant off-origin peak that is 33.59 % of the origin peak, indicating pseudo-translational symmetry.  The chance of finding a peak of this or larger height by random in a structure without pseudo-translational symmetry is equal to 7.8091e-04. The detected translational NCS is most likely also responsible for the elevated intensity ratio.  See the relevant section of the logfile for more details."
_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         99.41
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      48
_pdbx_vrpt_summary_diffraction.percent_free_reflections  5.65
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     14.29
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       2.38
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        30.71
_pdbx_vrpt_summary_diffraction.PDB_R                     0.23
_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_bond_outliers
_pdbx_vrpt_model_instance.count_angle_outliers
 1  1  1  A  1  DG   X    1  .  ?        2     5  
 2  1  1  A  2  DC   X    2  .  ?        ?     1  
 3  1  1  A  3  DA   X    3  .  ?        ?     1  
 4  1  1  A  4  DT   X    4  .  ?        ?     ?  
 5  1  1  A  5  DG   X    5  .  ?        ?     1  
 6  1  1  A  6  DC   X    6  .  ?        ?     1  
 7  1  1  A  7  DT   X    7  A  ?        ?     ?  
 8  1  1  A  7  DT   X    7  B  ?        ?     ?  
 9  1  2  B  .  NI   X  101  .  ?        ?     ?  
10  1  3  C  .  HOH  X  201  .  ?        ?     ?  
11  1  3  C  .  HOH  X  202  .  ?        ?     ?  
12  1  3  C  .  HOH  X  203  .  ?        ?     ?  
13  1  3  C  .  HOH  X  204  .  ?        ?     ?  
14  1  3  C  .  HOH  X  205  .  ?        ?     ?  
15  1  3  C  .  HOH  X  207  .  ?        ?     ?  
16  1  3  C  .  HOH  X  209  .  ?        ?     ?  
17  1  3  C  .  HOH  X  210  .  ?        ?     ?  
#
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  25.810    22  2.33    35  3.04  molprobity  1.000  
 2   2    11  29.880    21  1.50    32  2.51  molprobity  1.000  
 3   3    11  26.600    24  1.70    37  2.17  molprobity  1.000  
 4   4    12  26.190    22  1.79    34  1.95  molprobity  1.000  
 5   5    11  25.820    25  1.39    39  1.72  molprobity  1.000  
 6   6    11  35.060    21  1.37    32  2.07  molprobity  1.000  
 7   7    13  54.500    21  1.04    30  1.32  molprobity  1.000  
 8   8    13  54.500    21  1.04    30  1.32  molprobity  1.000  
 9   9     ?  23.530     ?     ?     ?     ?  ?           1.000  
10  10     ?  18.490     ?     ?     ?     ?  ?           0.500  
11  11     ?  18.320     ?     ?     ?     ?  ?           1.000  
12  12     ?  23.130     ?     ?     ?     ?  ?           1.000  
13  13     ?  17.010     ?     ?     ?     ?  ?           1.000  
14  14     ?  19.110     ?     ?     ?     ?  ?           1.000  
15  15     ?  21.260     ?     ?     ?     ?  ?           0.500  
16  16     ?  42.370     ?     ?     ?     ?  ?           1.000  
17  17     ?  30.720     ?     ?     ?     ?  ?           1.000  
#
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
1  1  C2  N2  1.391  1.341  0.010   5.01  
2  1  N7  C5  1.356  1.388  0.006  -5.38  
#
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  1  C4     C5     N7     113.160  110.800  0.400   5.90  
2  1  C6     C5     N7     127.062  130.400  0.600  -5.56  
3  1  N3     C2     N2     124.778  119.900  0.700   6.97  
4  1  "O4'"  "C1'"  N9     104.271  108.000  0.700  -5.33  
5  1  "O4'"  "C4'"  "C3'"  102.272  104.500  0.400  -5.57  
6  2  "O5'"  P      OP2    100.513  105.700  0.900  -5.76  
7  3  "O4'"  "C1'"  N9     111.579  108.000  0.700   5.11  
8  5  C4     C5     N7     108.748  110.800  0.400  -5.13  
9  6  "O5'"  P      OP2    118.326  110.700  1.200   6.36  
#
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  0.887  0.201   1.008  
 2   2  19  0.932  0.151  -0.013  
 3   3  21  0.930  0.171   0.283  
 4   4  20  0.950  0.175   0.272  
 5   5  22  0.965  0.136  -0.219  
 6   6  19  0.929  0.163   0.189  
 7   7  40  0.724  0.436   4.288  
 8   8  40  0.724  0.436   4.288  
 9   9   1  0.992  0.069       ?  
10  10   1  0.980  0.143       ?  
11  11   1  0.996  0.150       ?  
12  12   1  0.973  0.328       ?  
13  13   1  0.973  0.155       ?  
14  14   1  0.925  0.228       ?  
15  15   1  0.934  0.481       ?  
16  16   1  0.843  0.474       ?  
17  17   1  0.961  0.231       ?  
#
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          2.36                                                                  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  
##
