Data quality metrics extracted from 9dyx.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 9DYX 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
NSLS-II BEAMLINE 17-ID-2
Synchrotron site
_diffrn_source.pdbx_synchrotron_site
NSLS-II
Beamline
_diffrn_source.pdbx_synchrotron_beamline
17-ID-2
Temperature [K]
_diffrn.ambient_temp
100
Detector technology
_diffrn_detector.detector
PIXEL
Collection date
_diffrn_detector.pdbx_collection_date
2024-03-03
Detector
_diffrn_detector.type
DECTRIS EIGER X 16M
Wavelength(s) [Å]
_diffrn_source.pdbx_wavelength_list
0.979330
Software
Data reduction
_software.classification
XDS (20230630)
Data scaling
_software.classification
XSCALE (20230630)
Phasing
_software.classification
SHELXD (2013/2)
Refinement
_software.classification
PHENIX (1.21_5207)
General information
Spacegroup name
_symmetry.space_group_name_H-M
P -1
Unit cell parameters
_cell.length_{a,b,c} _cell.angle_{alpha,beta,gamma}
12.29 12.46 11.78 76.00 89.29 88.49
Wavelength
_diffrn_radiation_wavelength.wavelength
0.97933 Å

Data quality metricsOverallInnerShellOuterShell
Low resolution limit [Å] 
_reflns.d_resolution_low _reflns_shell.d_res_low
 12.290 12.290 1.130
High resolution limit [Å] 
_reflns.d_resolution_high _reflns_shell.d_res_high
 1.100 4.930 1.100
Rmerge 
_reflns.pdbx_Rmerge_I_obs _reflns_shell.Rmerge_I_obs
 0.080 0.033 0.427
Rmeas 
_reflns.pdbx_Rrim_I_all _reflns_shell.pdbx_Rrim_I_all
 0.113 0.047 0.604
  Rpim - - -
  Total number of observations - - -
Total number unique 
_reflns.number_obs _reflns_shell.number_unique_obs
 2331 30 102
<I/σ(I)> 
_reflns.pdbx_netI_over_sigmaI
 3.82 - -
Completeness [%] 
_reflns.percent_possible_obs
 84.7 - -
Multiplicity 
_reflns.pdbx_redundancy
 1.6 - -
CC(1/2) 
_reflns.pdbx_CC_half _reflns_shell.pdbx_CC_half
 0.992 0.998 0.764

Refinement
PDB entry ID
_entry.id
9DYX
Deposition date
_pdbx_database_status.recvd_initial_deposition_date
2024-10-15
Resolution
_refine.ls_d_res_low _refine.ls_d_res_high
12.3 - 1.100 Å
Rwork/Rfree
_refine.ls_R_factor_R_work _refine.ls_R_factor_R_free
0.1789 / 0.1775
Structure solution method
_refine.pdbx_method_to_determine_struct
AB INITIO PHASING