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Novel epoxide hydrolases belonging to the alpha/beta hydrolases superfamily in metagenomes from hot environments
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4INZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 7.5 291 200 mM Magnesium formate dehydrate, 100mM Sodium Hepes 7.5 20 % w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.92 35.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 163.94 α = 90 b = 46.22 β = 106.94 c = 73.87 γ = 90
Symmetry Space Group C 1 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 100 PIXEL DECTRIS PILATUS3 6M 2016-08-08 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) 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 1.39 39.51 98.2 0.035 15.6 3.2 104819 24.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.39 1.41 79 0.77 0.483 1.2 2.5
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4inz 1.39 39.51 99619 5200 98.19 0.17413 0.17257 0.20373 0.2031 RANDOM 24.809
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] -0.67 -0.18 0.61 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.458 r_dihedral_angle_4_deg 22.742 r_dihedral_angle_3_deg 16.15 r_long_range_B_refined 8.232 r_dihedral_angle_1_deg 5.772 r_mcangle_it 5.274 r_scbond_it 5.055 r_mcbond_it 3.716 r_angle_refined_deg 1.637 r_chiral_restr 0.114
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.458 r_dihedral_angle_4_deg 22.742 r_dihedral_angle_3_deg 16.15 r_long_range_B_refined 8.232 r_dihedral_angle_1_deg 5.772 r_mcangle_it 5.274 r_scbond_it 5.055 r_mcbond_it 3.716 r_angle_refined_deg 1.637 r_chiral_restr 0.114 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4792 Nucleic Acid Atoms Solvent Atoms 616 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement XDS data reduction xia2 data reduction Aimless data scaling MoRDa phasing