Data quality metrics extracted from 9vf8.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 9VF8 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
SSRF BEAMLINE BL17UM
Synchrotron site
_diffrn_source.pdbx_synchrotron_site
SSRF
Beamline
_diffrn_source.pdbx_synchrotron_beamline
BL17UM
Temperature [K]
_diffrn.ambient_temp
100
Detector technology
_diffrn_detector.detector
PIXEL
Collection date
_diffrn_detector.pdbx_collection_date
2023-05-27
Detector
_diffrn_detector.type
DECTRIS EIGER2 X 16M
Wavelength(s) [Å]
_diffrn_source.pdbx_wavelength_list
0.97918
Software
Data reduction
_software.classification
XDS
Data scaling #1
_software.classification
STARANISO
Data scaling #2
_software.classification
Aimless
Phasing
_software.classification
MOLREP
Refinement
_software.classification
REFMAC (5.8.0430)
General information
Spacegroup name
_symmetry.space_group_name_H-M
P 43 21 2
Unit cell parameters
_cell.length_{a,b,c} _cell.angle_{alpha,beta,gamma}
78.593 78.593 73.381 90.0 90.0 90.0
Wavelength
_diffrn_radiation_wavelength.wavelength
0.97918 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]
3.347 Å 1.0000 0.0000 0.0000
3.347 Å 0.0000 0.0000 0.0000
3.680 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
 44.303 44.303 3.767
High resolution limit [Å] 
_reflns.d_resolution_high _reflns_shell.d_res_high
 3.352 7.077 3.352
Rmerge 
_reflns.pdbx_Rmerge_I_obs _reflns_shell.Rmerge_I_obs
 0.530 0.121 4.174
Rmeas 
_reflns.pdbx_Rrim_I_all _reflns_shell.pdbx_Rrim_I_all
 0.543 0.124 4.267
Rpim 
_reflns.pdbx_Rpim_I_all _reflns_shell.pdbx_Rpim_I_all
 0.117 0.028 0.869
Total number of observations 
_reflns.pdbx_number_measured_all _reflns_shell.number_measured_all
 64878 8118 9731
Total number unique 
_reflns.number_obs _reflns_shell.number_unique_all
 2991 426 425
<I/σ(I)> 
_reflns.pdbx_netI_over_sigmaI _reflns_shell.meanI_over_sigI_obs
 5.13 7.67 1.34
Completeness (spherical) [%] 
_reflns.pdbx_percent_possible_spherical _reflns_shell.pdbx_percent_possible_spherical
 83.4 99.8 41.9
Completeness (ellipsoidal) [%] 
_reflns.pdbx_percent_possible_ellipsoidal _reflns_shell.pdbx_percent_possible_ellipsoidal
 91.1 99.8 59.4
Multiplicity 
_reflns.pdbx_redundancy _reflns_shell.pdbx_redundancy
 21.7 19.1 22.9
CC(1/2) 
_reflns.pdbx_CC_half _reflns_shell.pdbx_CC_half
 0.987 0.989 0.847
Anomalous completeness (spherical) 
_reflns.pdbx_percent_possible_spherical_anomalous _reflns_shell.pdbx_percent_possible_spherical_anomalous
 82.0 99.6 41.3
Anomalous completeness (ellipsoidal)
_reflns.pdbx_percent_possible_ellipsoidal_anomalous _reflns_shell.pdbx_percent_possible_ellipsoidal_anomalous
 89.9 99.6 58.1
Anomalous multiplicity 
_reflns.pdbx_redundancy_anomalous _reflns_shell.pdbx_redundancy_anomalous
 12.5 12.4 12.9
CC(ano) 
_reflns.pdbx_CC_half_anomalous _reflns_shell.pdbx_CC_half_anomalous
 0.075 0.059 -0.184
|DANO|/σ(DANO) 
_reflns.pdbx_absDiff_over_sigma_anomalous _reflns_shell.pdbx_absDiff_over_sigma_anomalous
 0.670 0.359 0.768

Refinement
PDB entry ID
_entry.id
9VF8
Deposition date
_pdbx_database_status.recvd_initial_deposition_date
2025-06-10
Resolution
_refine.ls_d_res_low _refine.ls_d_res_high
44.3 - 3.352 Å
Rwork/Rfree
_refine.ls_R_factor_R_work _refine.ls_R_factor_R_free
0.2422 / 0.2721
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