☰ Navigation Tabs
Crystal structure of hydroxynitrile lyase from Linum usitatissimum complexed with acetone cyanohydrin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7VB3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293.15 0.1 M BIS-TRIS, pH 6.5, 20% w/v polyethylene glycol monomethyl ether 5000
Crystal Properties Matthews coefficient Solvent content 2.13 42.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.12 α = 90 b = 51.57 β = 94.67 c = 170 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 2018-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.000 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 1.58 169.436 100 0.121 0.133 0.053 8.9 6.2 223351 223351
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 1.58 1.67 100 1.323 1.323 1.443 0.568 0.6 6.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7VB3 1.58 93.98 212183 11126 99.95 0.1722 0.1706 0.2046 0.203 RANDOM 23.96
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] -2.03 0.78 1.5 0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.598 r_dihedral_angle_4_deg 13.117 r_dihedral_angle_3_deg 13.012 r_dihedral_angle_1_deg 7.134 r_angle_refined_deg 1.593 r_angle_other_deg 1.38 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.598 r_dihedral_angle_4_deg 13.117 r_dihedral_angle_3_deg 13.012 r_dihedral_angle_1_deg 7.134 r_angle_refined_deg 1.593 r_angle_other_deg 1.38 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12532 Nucleic Acid Atoms Solvent Atoms 1137 Heterogen Atoms 380
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction Coot model building MOSFLM data reduction