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Cyclohexane epoxide low pH soak of 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 7.5 291 Morpheus crystallisation kit condition H8, 25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350 . The crystal was soaked for 2 hours in cryoprotectant containing 1mM of cyclohexane oxide at pH 4.5.
Crystal Properties Matthews coefficient Solvent content 2.31 46.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.851 α = 90 b = 47.33 β = 91.707 c = 142.611 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 2018-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 1.957 142.548 99.7 0.999 10 3.4 102758
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 1.957 1.991 99.7 0.303 3.4
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 1.957 142.548 92853 4502 99.681 0.208 0.2055 0.2055 0.2587 0.2586 54.15
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] -3.405 -0.919 5.268 -1.805
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.967 r_dihedral_angle_4_deg 21.336 r_dihedral_angle_3_deg 17.455 r_lrange_it 13.402 r_scangle_it 12.855 r_scbond_it 10.857 r_mcangle_it 10.434 r_mcbond_it 8.851 r_dihedral_angle_1_deg 6.608 r_angle_refined_deg 1.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.967 r_dihedral_angle_4_deg 21.336 r_dihedral_angle_3_deg 17.455 r_lrange_it 13.402 r_scangle_it 12.855 r_scbond_it 10.857 r_mcangle_it 10.434 r_mcbond_it 8.851 r_dihedral_angle_1_deg 6.608 r_angle_refined_deg 1.64 r_nbtor_refined 0.304 r_symmetry_nbd_refined 0.222 r_nbd_refined 0.214 r_xyhbond_nbd_refined 0.139 r_symmetry_xyhbond_nbd_refined 0.106 r_chiral_restr 0.104 r_ncsr_local_group_1 0.082 r_ncsr_local_group_3 0.081 r_ncsr_local_group_2 0.08 r_ncsr_local_group_5 0.078 r_ncsr_local_group_4 0.076 r_ncsr_local_group_6 0.071 r_bond_refined_d 0.01 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9543 Nucleic Acid Atoms Solvent Atoms 272 Heterogen Atoms 135
Software Software Software Name Purpose REFMAC refinement XDS data reduction autoPROC data processing XSCALE data scaling MOLREP phasing Coot model building PARROT phasing BUSTER refinement