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HYDROXYNITRILE LYASE FROM THE MILLIPEDE, Oxidus gracilis bound with (R)-(+)-ALPHA-HYDROXYBENZENE-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, 2.0 M ammonium sulfate, incubated in 25% (v/v) glycerol with a drop of BA and 2M potassium cyanide
Crystal Properties Matthews coefficient Solvent content 3.5 64.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.43 α = 90 b = 123.43 β = 90 c = 129.87 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 293.15 IMAGE PLATE RIGAKU 2017-08-16 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 64.94 99.5 0.066 8.2 3.1 74395
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 0.846
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 40.435 74350 3640 99.458 0.203 0.2019 0.233 0.2278 42.59
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] 0.782 0.391 0.782 -2.538
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.159 r_dihedral_angle_3_deg 15.716 r_dihedral_angle_2_deg 10.262 r_lrange_it 7.748 r_lrange_other 7.725 r_dihedral_angle_1_deg 7.666 r_scangle_it 6.368 r_scangle_other 6.171 r_mcangle_it 4.751 r_mcangle_other 4.751
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.159 r_dihedral_angle_3_deg 15.716 r_dihedral_angle_2_deg 10.262 r_lrange_it 7.748 r_lrange_other 7.725 r_dihedral_angle_1_deg 7.666 r_scangle_it 6.368 r_scangle_other 6.171 r_mcangle_it 4.751 r_mcangle_other 4.751 r_scbond_it 4.537 r_scbond_other 4.337 r_mcbond_it 3.501 r_mcbond_other 3.501 r_angle_refined_deg 1.546 r_angle_other_deg 0.526 r_nbd_refined 0.215 r_symmetry_nbd_other 0.194 r_xyhbond_nbd_refined 0.191 r_nbd_other 0.184 r_nbtor_refined 0.18 r_symmetry_nbd_refined 0.1 r_symmetry_xyhbond_nbd_other 0.099 r_symmetry_nbtor_other 0.086 r_symmetry_xyhbond_nbd_refined 0.078 r_chiral_restr 0.069 r_chiral_restr_other 0.02 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5058 Nucleic Acid Atoms Solvent Atoms 342 Heterogen Atoms 110
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling Coot model building