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Crystal Structure of Galactose Binding Protein from Yersinia pestis in the Complex with beta D Glucose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GAS PDBID 3GAS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 289 0.085M Tris:HCl pH 8.5, 25.5% (w/v) PEG 4000, 15% (v/v) Glycerol
Crystal Properties Matthews coefficient Solvent content 2.71 54.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.236 α = 90 b = 56.753 β = 90 c = 69.129 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2016-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97926 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.316 50 98.1 0.077 24.6 4.7 86602 18.81
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.32 1.34 80.3 0.516 0.741 1 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDBID 3GAS 1.316 36.252 1.34 86540 4349 97.76 0.1448 0.144 0.1459 0.1603 0.1621 random
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 18.1 f_angle_d 0.978 f_chiral_restr 0.088 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2350 Nucleic Acid Atoms Solvent Atoms 307 Heterogen Atoms 34
Software Software Software Name Purpose PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing