Data quality metrics extracted from 8vdj.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 8VDJ 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
APS BEAMLINE 17-ID
Synchrotron site
_diffrn_source.pdbx_synchrotron_site
APS
Beamline
_diffrn_source.pdbx_synchrotron_beamline
17-ID
Temperature [K]
_diffrn.ambient_temp
100
Detector technology
_diffrn_detector.detector
PIXEL
Collection date
_diffrn_detector.pdbx_collection_date
2022-07-10
Detector
_diffrn_detector.type
DECTRIS EIGER2 X 9M
Wavelength(s) [Å]
_diffrn_source.pdbx_wavelength_list
1.000
Software
Data processing
_software.classification
autoPROC (1.1.7 (20211020))
Data reduction
_software.classification
XDS (Feb 5, 2021 (BUILT 20210323))
Data scaling
_software.classification
Aimless (0.7.7)
Phasing
_software.classification
PHASER
Refinement
_software.classification
BUSTER (2.11.8 (8-JUN-2022))
General information
Spacegroup name
_symmetry.space_group_name_H-M
P 21 21 21
Unit cell parameters
_cell.length_{a,b,c} _cell.angle_{alpha,beta,gamma}
67.451 99.130 100.626 90.0 90.0 90.0
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]
1.920 Å 1.0000 0.0000 0.0000
2.832 Å 0.0000 0.0000 0.0000
2.309 Å 0.0000 0.0000 0.0000

Criteria used in determination of diffraction limits:
local <I/sigmaI>≥1.20

Data quality metricsOverallInnerShellOuterShell
Low resolution limit [Å] 
_reflns.d_resolution_low _reflns_shell.d_res_low
 70.618 70.618 2.219
High resolution limit [Å] 
_reflns.d_resolution_high _reflns_shell.d_res_high
 2.002 6.863 2.002
Rmerge 
_reflns.pdbx_Rmerge_I_obs _reflns_shell.Rmerge_I_obs
 0.126 0.044 0.833
Rmeas 
_reflns.pdbx_Rrim_I_all _reflns_shell.pdbx_Rrim_I_all
 0.137 0.048 0.908
Rpim 
_reflns.pdbx_Rpim_I_all _reflns_shell.pdbx_Rpim_I_all
 0.054 0.019 0.359
Total number of observations 
_reflns.pdbx_number_measured_all _reflns_shell.number_measured_all
 165074 8175 7910
Total number unique 
_reflns.number_obs _reflns_shell.number_unique_all
 25441 1272 1272
<I/σ(I)> 
_reflns.pdbx_netI_over_sigmaI _reflns_shell.meanI_over_sigI_obs
 9.73 25.39 2.17
Completeness (spherical) [%] 
_reflns.pdbx_percent_possible_spherical _reflns_shell.pdbx_percent_possible_spherical
 55.1 99.4 10.6
Completeness (ellipsoidal) [%] 
_reflns.pdbx_percent_possible_ellipsoidal _reflns_shell.pdbx_percent_possible_ellipsoidal
 85.8 99.4 63.3
Multiplicity 
_reflns.pdbx_redundancy _reflns_shell.pdbx_redundancy
 6.5 6.4 6.2
CC(1/2) 
_reflns.pdbx_CC_half _reflns_shell.pdbx_CC_half
 0.998 0.999 0.595
Anomalous completeness (spherical) 
_reflns.pdbx_percent_possible_spherical_anomalous _reflns_shell.pdbx_percent_possible_spherical_anomalous
 53.8 99.8 10.1
Anomalous completeness (ellipsoidal)
_reflns.pdbx_percent_possible_ellipsoidal_anomalous _reflns_shell.pdbx_percent_possible_ellipsoidal_anomalous
 85.0 99.8 62.9
Anomalous multiplicity 
_reflns.pdbx_redundancy_anomalous _reflns_shell.pdbx_redundancy_anomalous
 3.5 3.8 3.3
CC(ano) 
_reflns.pdbx_CC_half_anomalous _reflns_shell.pdbx_CC_half_anomalous
 -0.203 -0.426 0.001
|DANO|/σ(DANO) 
_reflns.pdbx_absDiff_over_sigma_anomalous _reflns_shell.pdbx_absDiff_over_sigma_anomalous
 0.747 0.513 0.753

Refinement
PDB entry ID
_entry.id
8VDJ
Deposition date
_pdbx_database_status.recvd_initial_deposition_date
2023-12-15
Resolution
_refine.ls_d_res_low _refine.ls_d_res_high
31.8 - 2.002 Å
Rwork/Rfree
_refine.ls_R_factor_R_work _refine.ls_R_factor_R_free
0.2352 / 0.2707
Structure solution method
_refine.pdbx_method_to_determine_struct
MOLECULAR REPLACEMENT
Starting model (for MR)
_refine.pdbx_starting_model
WARNING: no starting model (for MR) given