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Structure of thermostable eightfold mutant of limonene epoxide hydrolase from Rhodococcus erythropolis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NWW PDB ENTRY 1NWW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.4 294 1.44 M tri-sodium citrate, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.11 41.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.049 α = 90 b = 88.049 β = 90 c = 110.241 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 PIXEL DECTRIS PILATUS 6M 2012-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97625 ESRF ID29
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 1.45 76.253 99.9 0.073 0.024 18 9.9 87794 2.9 2.9 13.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.53 99.6 0.902 0.296 2.9 10 12648
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1NWW 1.5 44 2 75382 75382 4008 99.89 0.14261 0.14143 0.1466 0.16476 0.1677 RANDOM 18.991
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] 0.36 0.18 0.36 -1.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.83 r_dihedral_angle_4_deg 19.587 r_dihedral_angle_3_deg 12.727 r_dihedral_angle_1_deg 6.612 r_long_range_B_refined 5.979 r_long_range_B_other 5.979 r_scangle_other 4.942 r_scbond_it 3.344 r_scbond_other 3.343 r_mcangle_other 2.481
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.83 r_dihedral_angle_4_deg 19.587 r_dihedral_angle_3_deg 12.727 r_dihedral_angle_1_deg 6.612 r_long_range_B_refined 5.979 r_long_range_B_other 5.979 r_scangle_other 4.942 r_scbond_it 3.344 r_scbond_other 3.343 r_mcangle_other 2.481 r_mcangle_it 2.468 r_angle_refined_deg 2.275 r_mcbond_it 1.748 r_mcbond_other 1.729 r_angle_other_deg 0.976 r_chiral_restr 0.16 r_bond_refined_d 0.024 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3606 Nucleic Acid Atoms Solvent Atoms 362 Heterogen Atoms 57
Software Software Software Name Purpose tvx data collection PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling