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Crystal structure of Helicobacter pylori glutamate racemase bound to D-glutamate and a crystallographic artifact
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JFX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 4.5g/l HpGR 200mM Ammonium Acetate, 5mM D/L-Glutamate 20% DMSO 2.5mM ligand mixed 2:1 with INDEX G1 8% DMSO 1mM M3
Crystal Properties Matthews coefficient Solvent content 2.58 52.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.317 α = 90 b = 81.969 β = 90 c = 113.937 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER X 16M 2023-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E .9272 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.1 81.97 99.7 0.042 0.047 0.02 0.999 22.6 5.2 34681 42.51
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.16 99.9 0.523 0.577 0.24 0.906 5.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.1 66.54 1.35 34612 1671 99.5 0.1922 0.1901 0.1965 0.2306 0.2297 47.34
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 17.5544 f_angle_d 0.8603 f_chiral_restr 0.0548 f_bond_d 0.0076 f_plane_restr 0.0069
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3845 Nucleic Acid Atoms Solvent Atoms 168 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing