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Hydroxynitrile lyase from Parafonteria laminate complexed with benzaldehyde
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6JHC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293.15 potassium thiocyanate, sodium acetate PEG 8000 and PEG 1000, benzaldehyde
Crystal Properties Matthews coefficient Solvent content 2.15 42.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.304 α = 90 b = 33.13 β = 106.17 c = 72.018 γ = 90
Symmetry Space Group P 1 21 1
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 6M 2018-05-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.37 69.168 96.3 0.082 0.089 0.034 11.7 6.6 63260 63260
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.37 1.44 85.5 0.731 0.731 0.801 0.322 1.1 5.9
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 6JHC 1.37 34.88 60087 3169 96.22 0.1598 0.1589 0.1657 0.1761 0.1827 RANDOM 17.066
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.014 r_dihedral_angle_4_deg 15.795 r_dihedral_angle_3_deg 11.855 r_dihedral_angle_1_deg 7.526 r_angle_other_deg 1.379 r_angle_refined_deg 1.376 r_chiral_restr 0.061 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.014 r_dihedral_angle_4_deg 15.795 r_dihedral_angle_3_deg 11.855 r_dihedral_angle_1_deg 7.526 r_angle_other_deg 1.379 r_angle_refined_deg 1.376 r_chiral_restr 0.061 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2554 Nucleic Acid Atoms Solvent Atoms 434 Heterogen Atoms 28
Software Software Software Name Purpose XDS data reduction SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction