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Halogenated product of limonene epoxide turnover by epoxide hydrolase from metagenomic source ch65
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 condition C1; 40% v/v PEG 500* MME; 20% w/v PEG 20000. The crystal was incubated with 1mM mixture of cis (1R,2S,4R) and trans (1S,2R,4R) isomers of (+)-limonene oxide for 1 hour 20 mins to produce a halogenated product in the active site.
Crystal Properties Matthews coefficient Solvent content 2.09 41.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.83 α = 90 b = 46.11 β = 98.41 c = 93 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 2018-09-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 Diamond I04-1
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 1.49 51.263 99.1 0.998 8.8 3.2 93810
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 1.49 1.52 0.366
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 1.49 51.263 93795 4702 99.067 0.18 0.1779 0.1779 0.2156 0.2156 26.938
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] -0.91 -0.937 0.014 1.123
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.286 r_dihedral_angle_4_deg 20.713 r_dihedral_angle_3_deg 14.396 r_lrange_it 9.207 r_scangle_it 8.754 r_scbond_it 7.027 r_dihedral_angle_1_deg 5.999 r_mcangle_it 5.688 r_mcbond_it 4.62 r_angle_refined_deg 1.655
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.286 r_dihedral_angle_4_deg 20.713 r_dihedral_angle_3_deg 14.396 r_lrange_it 9.207 r_scangle_it 8.754 r_scbond_it 7.027 r_dihedral_angle_1_deg 5.999 r_mcangle_it 5.688 r_mcbond_it 4.62 r_angle_refined_deg 1.655 r_nbtor_refined 0.321 r_symmetry_nbd_refined 0.256 r_nbd_refined 0.225 r_symmetry_xyhbond_nbd_refined 0.199 r_xyhbond_nbd_refined 0.156 r_ncsr_local_group_1 0.123 r_chiral_restr 0.116 r_bond_refined_d 0.01 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4822 Nucleic Acid Atoms Solvent Atoms 432 Heterogen Atoms 79
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing BUSTER refinement PARROT phasing Coot model building