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Crystal structure of F128A mutant of an epoxide hydrolase from Bacillus megaterium complexed with its product (R)-3-[1]naphthyloxy-propane-1,2-diol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4G00
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 0.1 M Tris, 2.0 M (NH4)2SO4, 0.2 M Li2SO4, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.51 50.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.64 α = 90 b = 109.64 β = 90 c = 117.496 γ = 90
Symmetry Space Group P 41 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 IMAGE PLATE RIGAKU RAXIS IV++ mirrors 2012-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.9 50 100 0.221 0.221 8.337 7.4 121961 -3
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 2.9 3 100 0.79 7.4
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 SAD 4G00 2.9 45.25 16484 15898 804 96.68 0.1598 0.156 0.1604 0.2316 0.2291 5
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] -0.3344 -0.3344 0.6688
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.365 f_angle_d 1.117 f_chiral_restr 0.075 f_bond_d 0.008 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4719 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms 42
Software Software Software Name Purpose CrystalClear data collection PHASER phasing PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling