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HYDROXYNITRILE LYASE FROM THE MILLIPEDE, Oxidus gracilis complexed with (R)-2-Chloromandelonitrile
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 293.15 0.1 M BIS-TRIS (pH 5.5), 2.0 M ammonium sulfate incubated in 25% (v/v) glycerol with a drop of (R)-2-Chlorobenzaldehyde, and soaked with 2 M potassium cyanide
Crystal Properties Matthews coefficient Solvent content 3.51 64.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.79 α = 90 b = 123.79 β = 90 c = 129.5 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 61.9 99.2 0.052 10.4 3 74391
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 0.294
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 THROUGHOUT 6KFE 2.01 53.66 74380 3627 99.21 0.172 0.171 0.1709 0.1996 0.1996 29.239
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] 0.007 0.004 0.007 -0.024
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.829 r_dihedral_angle_3_deg 15.095 r_dihedral_angle_2_deg 10.387 r_dihedral_angle_1_deg 7.708 r_lrange_it 7.662 r_lrange_other 7.581 r_scangle_it 6.149 r_scangle_other 5.973 r_scbond_it 4.497 r_scbond_other 4.326
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.829 r_dihedral_angle_3_deg 15.095 r_dihedral_angle_2_deg 10.387 r_dihedral_angle_1_deg 7.708 r_lrange_it 7.662 r_lrange_other 7.581 r_scangle_it 6.149 r_scangle_other 5.973 r_scbond_it 4.497 r_scbond_other 4.326 r_mcangle_it 3.76 r_mcangle_other 3.759 r_mcbond_it 2.83 r_mcbond_other 2.829 r_angle_refined_deg 1.692 r_angle_other_deg 0.575 r_nbd_refined 0.225 r_symmetry_nbd_other 0.199 r_symmetry_xyhbond_nbd_other 0.198 r_xyhbond_nbd_refined 0.194 r_nbtor_refined 0.18 r_symmetry_xyhbond_nbd_refined 0.128 r_nbd_other 0.122 r_symmetry_nbtor_other 0.087 r_chiral_restr 0.08 r_symmetry_nbd_refined 0.066 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 5055 Nucleic Acid Atoms Solvent Atoms 474 Heterogen Atoms 121
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling Coot model building