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Limonene 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 6.5 291 Morpheus crystal screen condition C3, 40% v/v Glycerol; 20% w/v
PEG 4000 . The crystal was soaked for two hours in cryoprotectant containing 1mM mixture of cis (1R,2S,4R) and trans (1S,2R,4R) isomers of (+)-limonene oxide at pH 4.5.
Crystal Properties Matthews coefficient Solvent content 2.32 47.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.985 α = 90 b = 47.416 β = 91.66 c = 142.814 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 1.966 96.129 99.6 0.998 7.3 3.4 91956
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 1.966 2 0.322
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 1.966 96.129 91955 4467 99.594 0.233 0.2316 0.2349 0.2704 0.273 63.288
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] -5.799 -0.553 8.397 -2.561
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.337 r_dihedral_angle_4_deg 22 r_dihedral_angle_3_deg 16.069 r_lrange_it 10.003 r_scangle_it 8.892 r_scbond_it 6.749 r_mcangle_it 4.467 r_mcbond_it 3.455 r_dihedral_angle_1_deg 2.834 r_angle_refined_deg 1.635
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.337 r_dihedral_angle_4_deg 22 r_dihedral_angle_3_deg 16.069 r_lrange_it 10.003 r_scangle_it 8.892 r_scbond_it 6.749 r_mcangle_it 4.467 r_mcbond_it 3.455 r_dihedral_angle_1_deg 2.834 r_angle_refined_deg 1.635 r_nbtor_refined 0.285 r_nbd_refined 0.177 r_symmetry_nbd_refined 0.166 r_chiral_restr 0.115 r_ncsr_local_group_1 0.096 r_ncsr_local_group_4 0.093 r_ncsr_local_group_2 0.09 r_ncsr_local_group_6 0.09 r_ncsr_local_group_5 0.089 r_ncsr_local_group_3 0.085 r_symmetry_xyhbond_nbd_refined 0.065 r_xyhbond_nbd_refined 0.059 r_bond_refined_d 0.012 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9549 Nucleic Acid Atoms Solvent Atoms 231 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing BUSTER refinement Coot model building PARROT phasing