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Crystal structure of glutamate racemase from Thermus thermophilus in complex with D-glutamate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HJ7 PDB entry 5HJ7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 296 0.1 M Tris, pH 8.5, 2.5 M ammonium nitrate
Crystal Properties Matthews coefficient Solvent content 2.95 58.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.677 α = 90 b = 96.728 β = 90 c = 179.066 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 CMOS RDI CMOS_8M 2017-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.00 ALS 4.2.2
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 1.9 62.41 99.9 0.074 0.087 0.045 0.999 14.5 7 112287
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 1.9 2 100 1.4 1.664 0.891 0.741 1.3 6.7
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB entry 5HJ7 1.909 58.929 1.34 108287 5488 97.83 0.1872 0.1853 0.1899 0.2247 0.2254
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 14.851 f_angle_d 1.249 f_chiral_restr 0.069 f_bond_d 0.014 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7600 Nucleic Acid Atoms Solvent Atoms 950 Heterogen Atoms 112
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling PHASER phasing