Data quality metrics extracted from 7yds.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 7YDS 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
ROTATING ANODE
Source details
_diffrn_source.type
Cu FINE FOCUS
Temperature [K]
_diffrn.ambient_temp
100
Detector technology
_diffrn_detector.detector
PIXEL
Collection date
_diffrn_detector.pdbx_collection_date
2022-04-09
Detector
_diffrn_detector.type
DECTRIS PILATUS 200K
Wavelength(s) [Å]
_diffrn_source.pdbx_wavelength_list
1.54056
Software
Data processing
_software.classification
autoPROC
Data reduction
_software.classification
CrysalisPro
Data scaling
_software.classification
Aimless
Phasing
_software.classification
MLPHARE
Refinement
_software.classification
PHENIX (1.20.1_4487)
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}
71.076 94.880 96.069 90.0 90.0 90.0
Wavelength
_diffrn_radiation_wavelength.wavelength
1.54056 Å

Data quality metricsOverall
Low resolution limit [Å]
_reflns.d_resolution_low
13.140
High resolution limit [Å]
_reflns.d_resolution_high
2.300
Rmerge
_reflns.pdbx_Rmerge_I_obs
0.109
Rmeas
_reflns.pdbx_Rrim_I_all
0.154
Rpim
_reflns.pdbx_Rpim_I_all
0.109
  Total number of observations -
Total number unique
_reflns.number_obs
29320
<I/σ(I)>
_reflns.pdbx_netI_over_sigmaI
8.23
Completeness [%]
_reflns.percent_possible_obs
99.3
Multiplicity
_reflns.pdbx_redundancy
2.0
CC(1/2)
_reflns.pdbx_CC_half
0.983

Refinement
PDB entry ID
_entry.id
7YDS
Deposition date
_pdbx_database_status.recvd_initial_deposition_date
2022-07-04
Resolution
_refine.ls_d_res_low _refine.ls_d_res_high
13.1 - 2.300 Å
Rwork/Rfree
_refine.ls_R_factor_R_work _refine.ls_R_factor_R_free
0.1943 / 0.2461
Structure solution method
_refine.pdbx_method_to_determine_struct
MOLECULAR REPLACEMENT
Starting model (for MR)
_refine.pdbx_starting_model
6WKM, 3BIS