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HYDROXYNITRILE LYASE FROM THE MILLIPEDE, Oxidus gracilis IN ACETONITRILE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6KFE 6KFE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293.15 0.1 M BIS-TRIS containing 2.0 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 3.6 65.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.11 α = 90 b = 123.11 β = 90 c = 129.59 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 IMAGE PLATE RIGAKU 2017-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 2.01 61.56 99.4 0.055 10.6 3.1 73724
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 2.01 2.05 0.302
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6KFE 2.01 53.365 73708 3594 99.362 0.174 0.1729 0.2028 0.205 31.328
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] 0.611 0.305 0.611 -1.981
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.953 r_dihedral_angle_3_deg 15.264 r_dihedral_angle_2_deg 14.881 r_dihedral_angle_1_deg 7.745 r_lrange_it 7.555 r_lrange_other 7.424 r_scangle_it 6.172 r_scangle_other 5.913 r_scbond_it 4.546 r_scbond_other 4.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.953 r_dihedral_angle_3_deg 15.264 r_dihedral_angle_2_deg 14.881 r_dihedral_angle_1_deg 7.745 r_lrange_it 7.555 r_lrange_other 7.424 r_scangle_it 6.172 r_scangle_other 5.913 r_scbond_it 4.546 r_scbond_other 4.12 r_mcangle_it 3.901 r_mcangle_other 3.901 r_mcbond_it 2.949 r_mcbond_other 2.949 r_angle_refined_deg 1.69 r_angle_other_deg 0.564 r_symmetry_xyhbond_nbd_other 0.339 r_nbd_refined 0.22 r_symmetry_nbd_other 0.194 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.172 r_symmetry_xyhbond_nbd_refined 0.144 r_nbd_other 0.134 r_symmetry_nbd_refined 0.121 r_symmetry_nbtor_other 0.089 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5072 Nucleic Acid Atoms Solvent Atoms 350 Heterogen Atoms 145
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling Coot model building