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Structure of a thermostable elevenfold mutant of limonene epoxide hydrolase from Rhodococcus erythropolis, containing two stabilizing disulfide bonds
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, 50 mM sodium tartrate dihydrate, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.07 40.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.688 α = 90 b = 87.688 β = 90 c = 108.905 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 2013-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.999 ESRF ID23-1
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 1.8 44.25 99.5 0.068 0.042 10 3.5 45204 2.3 2.3 19.9
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 1.8 1.9 99.9 0.51 0.313 2.3 3.6 6552
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 1.8 44.25 2 42884 42884 2279 99.44 0.16266 0.16037 0.1734 0.20677 0.2141 RANDOM 28.115
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] -0.03 -0.02 -0.03 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.939 r_dihedral_angle_4_deg 15.216 r_dihedral_angle_3_deg 14.327 r_dihedral_angle_1_deg 7.727 r_long_range_B_refined 7.606 r_long_range_B_other 7.598 r_scangle_other 6.144 r_scbond_it 3.889 r_scbond_other 3.888 r_mcangle_other 3.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.939 r_dihedral_angle_4_deg 15.216 r_dihedral_angle_3_deg 14.327 r_dihedral_angle_1_deg 7.727 r_long_range_B_refined 7.606 r_long_range_B_other 7.598 r_scangle_other 6.144 r_scbond_it 3.889 r_scbond_other 3.888 r_mcangle_other 3.78 r_mcangle_it 3.77 r_mcbond_it 2.654 r_mcbond_other 2.637 r_angle_refined_deg 2.019 r_angle_other_deg 0.921 r_chiral_restr 0.128 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3603 Nucleic Acid Atoms Solvent Atoms 209 Heterogen Atoms 27
Software Software Software Name Purpose tvx data collection PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling