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Discovery and characterization of thermophilic limonene-1,2-epoxide hydrolases from hot spring metagenomic libraries. Tomsk-sample-Native
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NWW PDB ENTRY 1NWW
Crystallization Crystal Properties Matthews coefficient Solvent content 2.75 55.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.37 α = 90 b = 96.37 β = 90 c = 57.81 γ = 120
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 2M M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.26 41.7 99.9 0.06 20.4 10.1 82450 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.26 1.29 99.1 1.04 2.1 9.2
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1NWW 1.26 41.73 78330 4085 99.93 0.11846 0.11745 0.1315 0.13797 0.149 RANDOM 19.291
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] -0.11 -0.05 -0.11 0.35
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 37.827 r_dihedral_angle_2_deg 32.673 r_sphericity_bonded 16.186 r_dihedral_angle_4_deg 15.399 r_dihedral_angle_3_deg 13.305 r_dihedral_angle_1_deg 5.855 r_scbond_it 4.427 r_mcangle_it 3.418 r_mcbond_it 2.681 r_mcbond_other 2.549
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 37.827 r_dihedral_angle_2_deg 32.673 r_sphericity_bonded 16.186 r_dihedral_angle_4_deg 15.399 r_dihedral_angle_3_deg 13.305 r_dihedral_angle_1_deg 5.855 r_scbond_it 4.427 r_mcangle_it 3.418 r_mcbond_it 2.681 r_mcbond_other 2.549 r_rigid_bond_restr 1.363 r_angle_refined_deg 1.301 r_angle_other_deg 1.086 r_chiral_restr 0.08 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.004 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1960 Nucleic Acid Atoms Solvent Atoms 449 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement MOLREP phasing