data_6QIV

_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  6QIV
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    6QIV
_pdbx_vrpt_summary.PDB_deposition_date         2019-01-21
_pdbx_vrpt_summary.PDB_revision_number         4
_pdbx_vrpt_summary.PDB_revision_date           2024-01-24
_pdbx_vrpt_summary.RNA_suiteness               0.67
_pdbx_vrpt_summary.report_creation_date        2024-06-24:08:11
_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      "RNA (5'-R(*GP*CP*AP*GP*CP*AP*GP*C)-3')"  
2  non-polymer  CMBL4  
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  2.28  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         
4  RNAsuiteness_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   72.18  141614     ?     ?  
2  2  1   78.32    7711  2.26  2.30  
3  1  2  100.00  127900     ?     ?  
4  2  2  100.00    6849  2.26  2.30  
5  1  3   19.18  130704     ?     ?  
6  2  3   23.30    6980  2.26  2.30  
7  1  4   79.72    3102     ?     ?  
8  2  4   74.49    1121  1.86  2.70  
#
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      1.69
_pdbx_vrpt_summary_entity_geometry.bonds_RMSZ       0.99
_pdbx_vrpt_summary_entity_geometry.num_bonds_RMSZ   190
_pdbx_vrpt_summary_entity_geometry.num_angles_RMSZ  295
#
_pdbx_vrpt_summary_geometry.ordinal          1
_pdbx_vrpt_summary_geometry.clashscore       3.36
_pdbx_vrpt_summary_geometry.num_H_reduce     90
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ   190
_pdbx_vrpt_summary_geometry.bonds_RMSZ       0.99
_pdbx_vrpt_summary_geometry.num_angles_RMSZ  295
_pdbx_vrpt_summary_geometry.angles_RMSZ      1.69
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.Babinet_b                 85.410
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            28.969
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         48.912
_pdbx_vrpt_summary_diffraction.I_over_sigma              1.55(2.29A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        1430
_pdbx_vrpt_summary_diffraction.Babinet_k                 0.464
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.345
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.505
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.349
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.957
_pdbx_vrpt_summary_diffraction.twin_fraction             -h,l,k:0.000;-l,-k,-h:0.036
_pdbx_vrpt_summary_diffraction.DCC_R                     0.21
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.27
_pdbx_vrpt_summary_diffraction.EDS_R                     0.22
_pdbx_vrpt_summary_diffraction.EDS_res_high              2.28
_pdbx_vrpt_summary_diffraction.EDS_res_low               26.81
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[58.764,58.764,40.207,0.000,0.000,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.353
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The largest off-origin peak in the Patterson function is 16.80% 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         4
_pdbx_vrpt_summary_diffraction.centric_outliers          1
_pdbx_vrpt_summary_diffraction.data_completeness         99.86
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      143
_pdbx_vrpt_summary_diffraction.percent_free_reflections  10.00
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     0.00
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       2.28
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        26.80
_pdbx_vrpt_summary_diffraction.PDB_R                     0.20
_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_angle_outliers
_pdbx_vrpt_model_instance.count_clashes
_pdbx_vrpt_model_instance.count_mogul_torsion_outliers
_pdbx_vrpt_model_instance.ligand_of_interest
 1  1  1  A  1  G    A    1  .  ?        ?     2     ?  ?     
 2  1  1  A  2  C    A    2  .  ?        ?     ?     ?  ?     
 3  1  1  A  3  A    A    3  .  ?        ?     ?     ?  ?     
 4  1  1  A  4  G    A    4  .  ?        ?     ?     ?  ?     
 5  1  1  A  5  C    A    5  .  ?        2     ?     ?  ?     
 6  1  1  A  6  A    A    6  .  ?        1     ?     ?  ?     
 7  1  1  A  7  G    A    7  .  ?        1     ?     ?  ?     
 8  1  1  A  8  C    A    8  .  ?        ?     ?     ?  ?     
 9  1  2  B  .  J4H  A  101  .  ?        ?     ?     4  Y     
10  1  3  C  .  HOH  A  201  .  ?        ?     ?     ?  ?     
#
loop_
_pdbx_vrpt_model_instance_geometry.ordinal
_pdbx_vrpt_model_instance_geometry.instance_id
_pdbx_vrpt_model_instance_geometry.RNA_score
_pdbx_vrpt_model_instance_geometry.RNA_suite
_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  0.00  NotAvailable    12  45.330    23  0.90    37  1.24  molprobity  1.000  
 2   2  0.92  Rotameric       11  44.820    22  0.79    34  1.16  molprobity  1.000  
 3   3  0.83  Rotameric       11  43.190    25  1.05    39  1.25  molprobity  1.000  
 4   4  0.41  Rotameric       11  42.410    26  0.90    41  1.92  molprobity  1.000  
 5   5  0.68  Rotameric       11  41.080    22  1.02    34  2.22  molprobity  1.000  
 6   6  0.28  Rotameric       11  45.070    25  1.29    39  2.00  molprobity  1.000  
 7   7  0.76  Rotameric       11  47.550    26  0.92    41  1.73  molprobity  1.000  
 8   8  0.82  Rotameric       12  48.130    21  0.91    30  1.68  molprobity  1.000  
 9   9     ?  ?                ?  42.350    42  0.31    56  0.56  mogul       1.000  
10  10     ?  ?                ?  32.770     ?     ?     ?     ?  ?           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  H8      1  0.41  1.68  
2  1  "HO5'"  1  0.41  1.68  
#
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  5  C2  N3  C4  122.896  119.900  0.500   5.99  
2  5  N1  C2  O2  121.981  118.900  0.600   5.13  
3  6  C2  N3  C4  114.035  110.600  0.500   6.87  
4  7  N3  C2  N2  116.088  119.900  0.700  -5.45  
#
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  9  O3   C19  C20  C21    84.93  41.04  833  30.42   0.13  4.56  
2  9  C19  C20  C21  N8   -106.29  52.91  197  14.17  25.07  0.00  
3  9  C20  C21  N8   C22  -115.55  53.21  545  11.89   0.76  2.20  
4  9  C22  C23  C24  O4    -91.40  43.71  833  24.95   0.99  2.04  
#
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  20  0.926  0.147   0.193  
 2   2  20  0.941  0.110  -0.592  
 3   3  22  0.959  0.141   0.002  
 4   4  23  0.972  0.137  -0.010  
 5   5  20  0.958  0.132  -0.172  
 6   6  22  0.949  0.145   0.081  
 7   7  23  0.938  0.142   0.092  
 8   8  20  0.958  0.131  -0.191  
 9   9  38  0.934  0.145       ?  
10  10   1  0.876  0.176       ?  
#
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        "2022.3.0, CSD as543be (2022)"                                        Y  
3  eds          2.37.1                                                                Y  
4  dcc          '"2.27  (2023-04-10)"'                                                Y  
5  xtriage      1.20.1                                                                Y  
6  percentiles  "20191225.v01 (using entries in the PDB archive December 25th 2019)"  Y  
##
