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7BJ1

Crystal structure of SMYD3 with diperodon S enantiomer bound to allosteric site

Replaces:  6Z2R
Experimental procedure
Experimental methodSINGLE WAVELENGTH
Source typeSYNCHROTRON
Source detailsESRF BEAMLINE ID29
Synchrotron siteESRF
BeamlineID29
Temperature [K]100
Detector technologyPIXEL
Collection date2018-06-19
DetectorDECTRIS PILATUS 6M-F
Wavelength(s)0.976
Spacegroup nameP 21 21 21
Unit cell lengths60.909, 66.050, 107.277
Unit cell angles90.00, 90.00, 90.00
Refinement procedure
Resolution44.780 - 1.610
R-factor0.1734
Rwork0.172
R-free0.21000
Structure solution methodMOLECULAR REPLACEMENT
Starting model (for MR)5ccl
RMSD bond length0.008
RMSD bond angle1.140
Data reduction softwareXDS (b. 20180126)
Data scaling softwareAimless (0.7.1)
Phasing softwarePHASER
Refinement softwareREFMAC (5.8.0131)
Data quality characteristics
 OverallOuter shell
Low resolution limit [Å]56.2401.670
High resolution limit [Å]1.6101.610
Rmerge0.0671.528
Rmeas0.0751.714
Rpim0.0330.765
Number of reflections567435473
<I/σ(I)>12.3
Completeness [%]99.999.8
Redundancy5.14.8
CC(1/2)0.9990.466
Crystallization Conditions
crystal IDmethodpHtemperaturedetails
1VAPOR DIFFUSION, HANGING DROP8.25293Protein: 50 mM Tris, 150 mM NaCl, 1 mM (S)-diperodon, 10% DMSO, pH 8.0; reservoir: 100 mM Tris, 50 mM magnesium acetate, 11% PEG3350, pH 8.25

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PDB entries from 2024-05-15

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