Data quality metrics extracted from 1ybm.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 1YBM at RCSB, PDBe, PDBj

Experiment
Method
_exptl.method
X-RAY DIFFRACTION
Experimental protocol
_diffrn_radiation.pdbx_diffrn_protocol
MAD
Source type
_diffrn_source.source
SYNCHROTRON
Source details
_diffrn_source.type
APS BEAMLINE 14-ID-B
Synchrotron site
_diffrn_source.pdbx_synchrotron_site
APS
Beamline
_diffrn_source.pdbx_synchrotron_beamline
14-ID-B
Temperature [K]
_diffrn.ambient_temp
100
Detector technology
_diffrn_detector.detector
CCD
Collection date
_diffrn_detector.pdbx_collection_date
2004-08-08
Detector
_diffrn_detector.type
MAR CCD 165 mm
Wavelength(s) [Å]
_diffrn_source.pdbx_wavelength_list
0.97935, 0.97904, 0.96389
Software
Data reduction
_software.classification
DENZO (Zbyszek Otwinowski; zbyszek@mix.swmed.edu)
Data scaling
_software.classification
SCALEPACK (Zbyszek Otwinowski; zbyszek@mix.swmed.edu)
Phasing #1
_software.classification
SOLVE (2.06; 28-Dec-2003; Tom Terwilliger; terwilliger@LANL.gov)
Phasing #2
_software.classification
RESOLVE (2.06; 02-Jan-2004; Terwilliger, T. C; terwilliger@LANL.gov)
Refinement
_software.classification
REFMAC (refmac_5.2.0005; 24/04/2001; Murshudov, G.N.; ccp4@dl.ac.uk)
General information
Spacegroup name
_symmetry.space_group_name_H-M
P 21 21 2
Unit cell parameters
_cell.length_{a,b,c} _cell.angle_{alpha,beta,gamma}
74.634 77.286 92.864 90.0 90.0 90.0
Wavelength
_diffrn_radiation_wavelength.wavelength
0.979350.979040.96389 Å

Data quality metricsOverallInnerShellOuterShell
Low resolution limit [Å] 
_reflns.d_resolution_low _reflns_shell.d_res_low
 29.087 50.000 2.150
High resolution limit [Å] 
_reflns.d_resolution_high _reflns_shell.d_res_high
 2.096 5.180 2.100
Rmerge 
_reflns.pdbx_Rmerge_I_obs _reflns_shell.Rmerge_I_obs
 0.047 0.033 0.280
  Rmeas - - -
  Rpim - - -
Total number of observations 
_reflns_shell.number_measured_all
 - 1967 1878
Total number unique 
_reflns.number_obs
 29937 - -
<I/σ(I)> 
_reflns.pdbx_netI_over_sigmaI _reflns_shell.meanI_over_sigI_obs
 22.75 - 6.12
Completeness [%] 
_reflns.percent_possible_obs _reflns_shell.percent_possible_all
 93.0 84.8 88.3
Multiplicity 
_reflns.pdbx_redundancy _reflns_shell.pdbx_redundancy
 11.7 - 9.3
  CC(1/2) - - -

Refinement
PDB entry ID
_entry.id
1YBM
Deposition date
_pdbx_database_status.recvd_initial_deposition_date
2004-12-21
Resolution
_refine.ls_d_res_low _refine.ls_d_res_high
29.1 - 2.096 Å
Rwork/Rfree
_refine.ls_R_factor_R_work _refine.ls_R_factor_R_free
0.1888 / 0.2615
Structure solution method
_refine.pdbx_method_to_determine_struct
MAD