Data quality metrics extracted from 8gv0.cif.gz by aB_cif2table1 from BUSTER (Global Phasing Ltd.). See also the PDBx/mmCIF dictionary and a MXLIMS-compatible JSON representation.

Experimental information for 8GV0 at RCSB, PDBe, PDBj

Experiment
Method
_exptl.method
X-RAY DIFFRACTION
Experimental protocol
_diffrn_radiation.pdbx_diffrn_protocol
SINGLE WAVELENGTH
Source type
_diffrn_source.source
SYNCHROTRON
Source details
_diffrn_source.type
PHOTON FACTORY BEAMLINE BL-1A
Synchrotron site
_diffrn_source.pdbx_synchrotron_site
Photon Factory
Beamline
_diffrn_source.pdbx_synchrotron_beamline
BL-1A
Temperature [K]
_diffrn.ambient_temp
95
Detector technology
_diffrn_detector.detector
PIXEL
Collection date
_diffrn_detector.pdbx_collection_date
2021-12-13
Detector
_diffrn_detector.type
DECTRIS EIGER X 4M
Wavelength(s) [Å]
_diffrn_source.pdbx_wavelength_list
1.04500
Software
Data processing
_software.classification
autoPROC (1.1.7)
Data reduction
_software.classification
XDS (Jan 31, 2020)
Data scaling #1
_software.classification
Aimless (0.7.7)
Data scaling #2
_software.classification
STARANISO (2.3.63)
Phasing
_software.classification
PHASER
Refinement #1
_software.classification
PHENIX (1.20.1)
Refinement #2
_software.classification
BUSTER (2.11.8 (3-FEB-2022))
General information
Spacegroup name
_symmetry.space_group_name_H-M
P 1 21 1
Unit cell parameters
_cell.length_{a,b,c} _cell.angle_{alpha,beta,gamma}
40.937 162.082 139.014 90.00 98.05 90.00
Wavelength
_diffrn_radiation_wavelength.wavelength
1.04500 Å

Diffraction limits
_reflns.pdbx_aniso_diffraction_limit_{1,2,3}
Principal axes of ellipsoid fitted to diffraction cut-off surface
_reflns.pdbx_aniso_diffraction_limit_axis_{1,2,3}_ortho[1..3]
3.186 Å 0.9356 0.0000 -0.3530
3.842 Å 0.0000 0.0000 0.0000
3.782 Å 0.0000 0.0000 0.0000

Data quality metricsOverallInnerShellOuterShell
Low resolution limit [Å] 
_reflns.d_resolution_low _reflns_shell.d_res_low
 137.644 137.644 3.705
High resolution limit [Å] 
_reflns.d_resolution_high _reflns_shell.d_res_high
 3.192 10.268 3.192
Rmerge 
_reflns.pdbx_Rmerge_I_obs _reflns_shell.Rmerge_I_obs
 0.521 0.123 1.376
Rmeas 
_reflns.pdbx_Rrim_I_all _reflns_shell.pdbx_Rrim_I_all
 0.563 0.132 1.487
Rpim 
_reflns.pdbx_Rpim_I_all _reflns_shell.pdbx_Rpim_I_all
 0.212 0.049 0.557
Total number of observations 
_reflns.pdbx_number_measured_all _reflns_shell.number_measured_all
 127817 6486 6171
Total number unique 
_reflns.number_obs _reflns_shell.number_unique_all
 18205 909 911
<I/σ(I)> 
_reflns.pdbx_netI_over_sigmaI _reflns_shell.meanI_over_sigI_obs
 4.10 11.31 1.64
Completeness (spherical) [%] 
_reflns.pdbx_percent_possible_spherical _reflns_shell.pdbx_percent_possible_spherical
 61.0 99.6 8.5
Completeness (ellipsoidal) [%] 
_reflns.pdbx_percent_possible_ellipsoidal _reflns_shell.pdbx_percent_possible_ellipsoidal
 86.4 99.6 37.7
Multiplicity 
_reflns.pdbx_redundancy _reflns_shell.pdbx_redundancy
 7.0 7.1 6.8
CC(1/2) 
_reflns.pdbx_CC_half _reflns_shell.pdbx_CC_half
 0.929 0.988 0.552
Anomalous completeness (spherical) 
_reflns.pdbx_percent_possible_spherical_anomalous _reflns_shell.pdbx_percent_possible_spherical_anomalous
 60.4 99.9 8.1
Anomalous completeness (ellipsoidal)
_reflns.pdbx_percent_possible_ellipsoidal_anomalous _reflns_shell.pdbx_percent_possible_ellipsoidal_anomalous
 86.0 99.9 36.6
Anomalous multiplicity 
_reflns.pdbx_redundancy_anomalous _reflns_shell.pdbx_redundancy_anomalous
 3.6 3.7 3.5
CC(ano) 
_reflns.pdbx_CC_half_anomalous _reflns_shell.pdbx_CC_half_anomalous
 0.000 -0.016 -0.018
|DANO|/σ(DANO) 
_reflns.pdbx_absDiff_over_sigma_anomalous _reflns_shell.pdbx_absDiff_over_sigma_anomalous
 0.793 0.727 0.782

Refinement
PDB entry ID
_entry.id
8GV0
Deposition date
_pdbx_database_status.recvd_initial_deposition_date
2022-09-14
Resolution
_refine.ls_d_res_low _refine.ls_d_res_high
42.5 - 3.192 Å
Rwork/Rfree
_refine.ls_R_factor_R_work _refine.ls_R_factor_R_free
0.1960 / 0.3098
Structure solution method
_refine.pdbx_method_to_determine_struct
MOLECULAR REPLACEMENT
Starting model (for MR)
_refine.pdbx_starting_model
5DK3