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7VFM

Crystal structure of SdgB (UDP and SD peptide-binding form)

Replaces:  7EC4
Experimental procedure
Experimental methodSINGLE WAVELENGTH
Source typeSYNCHROTRON
Source detailsPAL/PLS BEAMLINE 7A (6B, 6C1)
Synchrotron sitePAL/PLS
Beamline7A (6B, 6C1)
Temperature [K]100
Detector technologyCCD
Collection date2014-09-29
DetectorADSC QUANTUM 270
Wavelength(s)0.9794
Spacegroup nameP 1 21 1
Unit cell lengths42.660, 206.662, 65.935
Unit cell angles90.00, 104.83, 90.00
Refinement procedure
Resolution29.850 - 2.280
R-factor0.2162
Rwork0.213
R-free0.27370
Structure solution methodMOLECULAR REPLACEMENT
Starting model (for MR)7ec1
Data reduction softwareHKL-2000
Data scaling softwareHKL-2000
Phasing softwareMOLREP
Refinement softwarePHENIX (1.19.2_4158)
Data quality characteristics
 OverallOuter shell
Low resolution limit [Å]50.0002.320
High resolution limit [Å]2.2802.280
Number of reflections498002418
<I/σ(I)>27.5
Completeness [%]99.6
Redundancy4.6
CC(1/2)0.9950.710
Crystallization Conditions
crystal IDmethodpHtemperaturedetails
1VAPOR DIFFUSION, SITTING DROP2870.2 M MgCl2, 0.1 M Tris-HCl (pH 8.5), and 25% (w/v) polyethylene glycol (PEG) 3,350 quick-soaked with 6.14 mM UDP and 2.45 mM 5-mer SD-repeat peptide (DSDSD)

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PDB entries from 2024-05-15

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