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HYDROXYNITRILE LYASE FROM THE MILLIPEDE
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% glycerol with a drop of benzaldehyde and 2 M potassium cyanide
Crystal Properties Matthews coefficient Solvent content 3.49 64.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.16 α = 90 b = 123.16 β = 90 c = 130.14 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 61.58 99.9 0.069 7.9 3 74529
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 0.069
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 49.396 74513 3631 99.893 0.208 0.2061 0.2057 0.2349 0.2345 39.04
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] 0.323 0.162 0.323 -1.049
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.57 r_dihedral_angle_3_deg 14.696 r_dihedral_angle_2_deg 10.637 r_dihedral_angle_1_deg 7.923 r_lrange_other 7.827 r_lrange_it 7.824 r_scangle_it 6.165 r_scangle_other 5.907 r_mcangle_it 4.807 r_mcangle_other 4.806
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.57 r_dihedral_angle_3_deg 14.696 r_dihedral_angle_2_deg 10.637 r_dihedral_angle_1_deg 7.923 r_lrange_other 7.827 r_lrange_it 7.824 r_scangle_it 6.165 r_scangle_other 5.907 r_mcangle_it 4.807 r_mcangle_other 4.806 r_scbond_it 4.63 r_scbond_other 4.25 r_mcbond_it 3.503 r_mcbond_other 3.502 r_angle_refined_deg 1.541 r_angle_other_deg 0.514 r_nbd_refined 0.219 r_xyhbond_nbd_refined 0.219 r_symmetry_xyhbond_nbd_other 0.216 r_symmetry_nbd_other 0.198 r_nbtor_refined 0.18 r_symmetry_nbd_refined 0.149 r_nbd_other 0.148 r_symmetry_xyhbond_nbd_refined 0.132 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.069 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 5072 Nucleic Acid Atoms Solvent Atoms 339 Heterogen Atoms 125
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling Coot model building