Data quality metrics extracted from 8gv1.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 8GV1 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
SPRING-8 BEAMLINE BL45XU
Synchrotron site
_diffrn_source.pdbx_synchrotron_site
SPring-8
Beamline
_diffrn_source.pdbx_synchrotron_beamline
BL45XU
Temperature [K]
_diffrn.ambient_temp
100
Detector technology
_diffrn_detector.detector
PIXEL
Collection date
_diffrn_detector.pdbx_collection_date
2021-10-23
Detector
_diffrn_detector.type
DECTRIS PILATUS3 6M
Wavelength(s) [Å]
_diffrn_source.pdbx_wavelength_list
1.00000
Software
Data processing
_software.classification
autoPROC
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
C 1 2 1
Unit cell parameters
_cell.length_{a,b,c} _cell.angle_{alpha,beta,gamma}
84.890 62.298 81.636 90.00 105.55 90.00
Wavelength
_diffrn_radiation_wavelength.wavelength
1.00000 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]
1.186 Å 0.8536 0.0000 0.5211
1.300 Å 0.0000 0.0000 0.0000
1.293 Å 0.0000 0.0000 0.0000

Data quality metricsOverallInnerShellOuterShell
Low resolution limit [Å] 
_reflns.d_resolution_low _reflns_shell.d_res_low
 49.558 49.558 1.289
High resolution limit [Å] 
_reflns.d_resolution_high _reflns_shell.d_res_high
 1.186 3.508 1.186
Rmerge 
_reflns.pdbx_Rmerge_I_obs _reflns_shell.Rmerge_I_obs
 0.036 0.025 0.967
Rmeas 
_reflns.pdbx_Rrim_I_all _reflns_shell.pdbx_Rrim_I_all
 0.041 0.028 1.069
Rpim 
_reflns.pdbx_Rpim_I_all _reflns_shell.pdbx_Rpim_I_all
 0.018 0.013 0.452
Total number of observations 
_reflns.pdbx_number_measured_all _reflns_shell.number_measured_all
 495020 23784 28790
Total number unique 
_reflns.number_obs _reflns_shell.number_unique_all
 104460 5223 5226
<I/σ(I)> 
_reflns.pdbx_netI_over_sigmaI _reflns_shell.meanI_over_sigI_obs
 11.42 28.89 1.44
Completeness (spherical) [%] 
_reflns.pdbx_percent_possible_spherical _reflns_shell.pdbx_percent_possible_spherical
 78.8 99.4 17.8
Completeness (ellipsoidal) [%] 
_reflns.pdbx_percent_possible_ellipsoidal _reflns_shell.pdbx_percent_possible_ellipsoidal
 93.5 99.4 57.2
Multiplicity 
_reflns.pdbx_redundancy _reflns_shell.pdbx_redundancy
 4.7 4.5 5.5
CC(1/2) 
_reflns.pdbx_CC_half _reflns_shell.pdbx_CC_half
 0.999 0.999 0.610
Anomalous completeness (spherical) 
_reflns.pdbx_percent_possible_spherical_anomalous _reflns_shell.pdbx_percent_possible_spherical_anomalous
 76.8 98.1 17.6
Anomalous completeness (ellipsoidal)
_reflns.pdbx_percent_possible_ellipsoidal_anomalous _reflns_shell.pdbx_percent_possible_ellipsoidal_anomalous
 91.3 98.1 57.1
Anomalous multiplicity 
_reflns.pdbx_redundancy_anomalous _reflns_shell.pdbx_redundancy_anomalous
 2.4 2.4 2.8
CC(ano) 
_reflns.pdbx_CC_half_anomalous _reflns_shell.pdbx_CC_half_anomalous
 -0.117 -0.126 0.011
|DANO|/σ(DANO) 
_reflns.pdbx_absDiff_over_sigma_anomalous _reflns_shell.pdbx_absDiff_over_sigma_anomalous
 0.615 0.416 0.647

Refinement
PDB entry ID
_entry.id
8GV1
Deposition date
_pdbx_database_status.recvd_initial_deposition_date
2022-09-14
Resolution
_refine.ls_d_res_low _refine.ls_d_res_high
49.6 - 1.186 Å
Rwork/Rfree
_refine.ls_R_factor_R_work _refine.ls_R_factor_R_free
0.2059 / 0.2265
Structure solution method
_refine.pdbx_method_to_determine_struct
MOLECULAR REPLACEMENT
Starting model (for MR)
_refine.pdbx_starting_model
5DK3