data_7RVL

_audit_conform.dict_name      mmcif_pdbx_vrpt.dic
_audit_conform.dict_version   0.068
_audit_conform.dict_location  https://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx_vrpt.dic
#
_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  7RVL
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   "electron crystallography"
#
_pdbx_vrpt_summary.entry_id                    7RVL
_pdbx_vrpt_summary.PDB_deposition_date         2021-08-18
_pdbx_vrpt_summary.PDB_revision_number         2
_pdbx_vrpt_summary.PDB_revision_date           2024-05-22
_pdbx_vrpt_summary.report_creation_date        2025-02-20:13:36
_pdbx_vrpt_summary.attempted_validation_steps  molprobity,validation-pack,xtriage,eds_mogul,validation_schema,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  "Major prion protein"  
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  pdb  
2  all  "electron microscopy"  
#
loop_
_pdbx_vrpt_percentile_type.id
_pdbx_vrpt_percentile_type.type
1  all_atom_clashscore           
2  Ramachandran_outlier_percent  
3  rotamer_outliers_percent      
4  RSRZ_outliers_percent         
5  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  210492  ?     ?     
 2  2  1   99.83   15764  ?     ?     
 3  1  2  100.00  207382  ?     ?     
 4  2  2  100.00   16835  ?     ?     
 5  1  3  100.00  206894  ?     ?     
 6  2  3  100.00   16415  ?     ?     
 7  1  4    2.66  164674  ?     ?     
 8  2  4   37.04      54  ?     ?     
 9  1  5   46.68  164678  ?     ?     
10  2  5   95.74      53  ?     ?     
#
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  
3  5  3  A  1  1  A  100.00  
4  6  3  A  1  1  A  100.00  
5  7  4  A  1  1  A    2.64  
6  8  4  A  1  1  A    2.18  
#
_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      0.57
_pdbx_vrpt_summary_entity_geometry.bonds_RMSZ       0.54
_pdbx_vrpt_summary_entity_geometry.num_bonds_RMSZ   78
_pdbx_vrpt_summary_entity_geometry.num_angles_RMSZ  104
#
_pdbx_vrpt_summary_geometry.ordinal                        1
_pdbx_vrpt_summary_geometry.percent_ramachandran_outliers  0.00
_pdbx_vrpt_summary_geometry.percent_rotamer_outliers       0.00
_pdbx_vrpt_summary_geometry.clashscore                     0.00
_pdbx_vrpt_summary_geometry.num_H_reduce                   63
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ                 78
_pdbx_vrpt_summary_geometry.bonds_RMSZ                     0.54
_pdbx_vrpt_summary_geometry.num_angles_RMSZ                104
_pdbx_vrpt_summary_geometry.angles_RMSZ                    0.57
#
_pdbx_vrpt_summary_diffraction.exp_method                "electron crystallography"
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            34.321
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         4.336
_pdbx_vrpt_summary_diffraction.I_over_sigma              3.10(1.00A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        2733
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.450
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.492
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.403
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.934
_pdbx_vrpt_summary_diffraction.twin_fraction             h,-h-k,-l:0.270;-h,-k,l:0.005;-h,h+k,-l:0.000
_pdbx_vrpt_summary_diffraction.DCC_R                     0.2139
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.2353
_pdbx_vrpt_summary_diffraction.EDS_R                     0.2214
_pdbx_vrpt_summary_diffraction.EDS_res_high              1.00
_pdbx_vrpt_summary_diffraction.EDS_res_low               10.14
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[3.862,6.481,5.684,-0.371,0.577,-1.905]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.490
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The analyses of the Patterson function reveals a significant off-origin peak that is 55.34 % 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 3.2072e-05. 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         86.93
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      649
_pdbx_vrpt_summary_diffraction.percent_free_reflections  9.02
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     22.22
_pdbx_vrpt_summary_diffraction.density_fitness_version   1.0.11
_pdbx_vrpt_summary_diffraction.CCP4_version              "9.0.004 (Gargrove)"
#
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
 1  1  1  A  1  GLU  A  168  .  ?     
 2  1  1  A  2  PHE  A  169  .  ?     
 3  1  1  A  3  SER  A  170  .  ?     
 4  1  1  A  4  ASN  A  171  .  ?     
 5  1  1  A  5  GLN  A  172  .  ?     
 6  1  1  A  6  ASN  A  173  .  ?     
 7  1  1  A  7  ASN  A  174  .  ?     
 8  1  1  A  8  PHE  A  175  .  ?     
 9  1  1  A  9  VAL  A  176  .  ?     
10  1  2  B  .  HOH  A  201  .  ?     
#
loop_
_pdbx_vrpt_model_instance_geometry.ordinal
_pdbx_vrpt_model_instance_geometry.instance_id
_pdbx_vrpt_model_instance_geometry.rotamer_class
_pdbx_vrpt_model_instance_geometry.phi
_pdbx_vrpt_model_instance_geometry.psi
_pdbx_vrpt_model_instance_geometry.ramachandran_class
_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  tt0        ?      ?  ?           5  17.590     9  0.59    12  0.54  molprobity  1.000  
 2   2  t80   -123.7  115.4  Favored     9   7.120    12  0.39    16  0.69  molprobity  1.000  
 3   3  m     -125.6  125.5  Favored     5   5.980     6  0.43     8  0.41  molprobity  1.000  
 4   4  t30   -145.7  129.6  Favored     6   2.960     8  0.47    11  0.55  molprobity  1.000  
 5   5  tm0?  -146.7  133.7  Favored     8   2.100     9  0.62    12  0.66  molprobity  1.000  
 6   6  m-80  -141.3  142.3  Favored     6   4.050     8  0.92    11  0.53  molprobity  1.000  
 7   7  m-20  -119.0  131.8  Favored     6   4.400     8  0.46    11  0.78  molprobity  1.000  
 8   8  m-85  -126.5  113.7  Favored     9   7.700    12  0.48    16  0.35  molprobity  1.000  
 9   9  t          ?      ?  ?           9  17.500     6  0.17     7  0.28  molprobity  1.000  
10  10  ?          ?      ?  ?           ?  24.200     ?     ?     ?     ?  ?           1.000  
#
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
_pdbx_vrpt_model_instance_density.EDIAm
_pdbx_vrpt_model_instance_density.OPIA
 1   1  17  0.779  0.161  2.080  0.181    0.000  
 2   2  20  0.923  0.076  1.204  0.892  100.000  
 3   3  11  0.895  0.090  1.067  0.860  100.000  
 4   4  14  0.871  0.093  1.152  0.887  100.000  
 5   5  17  0.933  0.075  0.239  0.831   77.780  
 6   6  14  0.904  0.095  1.215  0.821   62.500  
 7   7  14  0.899  0.087  0.962  0.869   87.500  
 8   8  20  0.921  0.094  1.987  0.820   81.820  
 9   9  16  0.755  0.164  5.139  0.183   42.860  
10  10   1  0.796  0.197      ?  0.354    0.000  
#
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          3.0                                                                   Y  
3  dcc          '"2.29  (2024-07-11))"'                                               Y  
4  xtriage      1.21                                                                  Y  
5  percentiles  "20231227.v01 (using entries in the PDB archive December 27th 2023)"  Y  
##
