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Glutamate Racemase (MurI) from Mycobacterium smegmatis with bound D-glutamate, 1.8 Angstrom resolution, X-ray diffraction
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GZM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 18% PEG 3350, 0.2 M NaI
Crystal Properties Matthews coefficient Solvent content 2.38 48.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.1 α = 90 b = 90.1 β = 90 c = 101.7 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 93 IMAGE PLATE RIGAKU RAXIS IV++ confocal mirrors 2014-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.542
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.76 52.4 97 0.109 11 6.9 54647 21.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.76 1.82 90.2 0.325 4.5 6.1
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2GZM 1.76 52.4 1.38 54624 2777 96.81 0.1701 0.1727 0.2053 0.2087 Random selection
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 13.545 f_angle_d 0.848 f_chiral_restr 0.055 f_bond_d 0.006 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4017 Nucleic Acid Atoms Solvent Atoms 548 Heterogen Atoms 23
Software Software Software Name Purpose PHENIX refinement CrystalClear data collection CrystalClear phasing CrystalClear data reduction CrystalClear data scaling PHASER phasing