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Cyclohexane epoxide soak of epoxide hydrolase from metagenomic source ch65 resulting in halogenated compound in the active site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NG7 5ng7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 291 Morpheus crystallisation kit C1; 40% v/v PEG 500* MME; 20% w/v PEG 20000, thecrystal was soaked with cyclohexane epoxide substrate at pH 6.5 for 2 hours to produce halogenated product.
Crystal Properties Matthews coefficient Solvent content 2.09 41.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.21 α = 90 b = 46.19 β = 98 c = 92.14 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2018-08-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.61 46.19 97.5 0.999 12.2 3.2 73190
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.61 1.64 0.43
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5ng7 1.61 45.663 73175 3603 97.448 0.182 0.1803 0.1803 0.2226 0.2226 33.552
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] -1.032 -1.534 0.244 1.173
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.828 r_dihedral_angle_4_deg 23.874 r_dihedral_angle_3_deg 16.664 r_lrange_it 11.018 r_scangle_it 10.36 r_scbond_it 8.969 r_mcangle_it 6.892 r_mcbond_it 5.896 r_dihedral_angle_1_deg 5.804 r_angle_refined_deg 1.727
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.828 r_dihedral_angle_4_deg 23.874 r_dihedral_angle_3_deg 16.664 r_lrange_it 11.018 r_scangle_it 10.36 r_scbond_it 8.969 r_mcangle_it 6.892 r_mcbond_it 5.896 r_dihedral_angle_1_deg 5.804 r_angle_refined_deg 1.727 r_nbtor_refined 0.32 r_symmetry_nbd_refined 0.28 r_nbd_refined 0.23 r_symmetry_xyhbond_nbd_refined 0.179 r_xyhbond_nbd_refined 0.174 r_chiral_restr 0.118 r_ncsr_local_group_1 0.116 r_bond_refined_d 0.011 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4839 Nucleic Acid Atoms Solvent Atoms 300 Heterogen Atoms 83
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing Coot model building BUSTER refinement PARROT phasing