Data quality metrics extracted from 6pdm.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 6PDM 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 24-ID-E
Synchrotron site
_diffrn_source.pdbx_synchrotron_site
APS
Beamline
_diffrn_source.pdbx_synchrotron_beamline
24-ID-E
Temperature [K]
_diffrn.ambient_temp
100
Detector technology
_diffrn_detector.detector
PIXEL
Collection date
_diffrn_detector.pdbx_collection_date
2019-02-21
Detector
_diffrn_detector.type
DECTRIS EIGER X 16M
Wavelength(s) [Å]
_diffrn_source.pdbx_wavelength_list
0.97918
Software
Data reduction
_software.classification
XDS
Data scaling
_software.classification
Aimless (0.7.4)
Phasing
_software.classification
MR-Rosetta
Refinement
_software.classification
BUSTER (2.10.2)
General information
Spacegroup name
_symmetry.space_group_name_H-M
P 1 21 1
Unit cell parameters
_cell.length_{a,b,c} _cell.angle_{alpha,beta,gamma}
64.812 83.802 65.711 90.00 98.16 90.00
Wavelength
_diffrn_radiation_wavelength.wavelength
0.97918 Å

Data quality metricsOverallInnerShellOuterShell
Low resolution limit [Å] 
_reflns.d_resolution_low _reflns_shell.d_res_low
 65.050 65.050 2.490
High resolution limit [Å] 
_reflns.d_resolution_high _reflns_shell.d_res_high
 2.400 8.970 2.400
Rmerge 
_reflns.pdbx_Rmerge_I_obs _reflns_shell.Rmerge_I_obs
 0.072 0.022 1.208
Rmeas 
_reflns.pdbx_Rrim_I_all _reflns_shell.pdbx_Rrim_I_all
 0.085 0.026 1.419
Rpim 
_reflns.pdbx_Rpim_I_all _reflns_shell.pdbx_Rpim_I_all
 0.045 0.014 0.739
Total number of observations 
_reflns.pdbx_number_measured_all _reflns_shell.number_measured_all
 92810 1846 9728
Total number unique 
_reflns.number_obs _reflns_shell.number_unique_obs
 27005 551 2704
<I/σ(I)> 
_reflns.pdbx_netI_over_sigmaI _reflns_shell.pdbx_netI_over_sigmaI_obs
 11.00 45.50 0.90
Completeness [%] 
_reflns.percent_possible_obs _reflns_shell.percent_possible_all
 98.7 99.6 94.7
Multiplicity 
_reflns.pdbx_redundancy _reflns_shell.pdbx_redundancy
 3.4 3.4 3.6
CC(1/2) 
_reflns.pdbx_CC_half _reflns_shell.pdbx_CC_half
 0.998 0.999 0.468

Refinement
PDB entry ID
_entry.id
6PDM
Deposition date
_pdbx_database_status.recvd_initial_deposition_date
2019-06-19
Resolution
_refine.ls_d_res_low _refine.ls_d_res_high
65.0 - 2.450 Å
Rwork/Rfree
_refine.ls_R_factor_R_work _refine.ls_R_factor_R_free
0.2160 / 0.2600
Structure solution method
_refine.pdbx_method_to_determine_struct
MOLECULAR REPLACEMENT
Starting model (for MR)
_refine.pdbx_starting_model
PHENIX.MR_ROSETTA with PDB entry 4C4A