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Crystal Structure of Hydroxynitrile Lyase from Sorghum bicolor in Complex with Inhibitor Benzoic Acid: a novel cyanogenic enzyme
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SC2 PDB ENTRY 3SC2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.4 100MM NA-CITRATE PH 5.4 USING 1.6 M AMMONIUM SULFATE
Crystal Properties Matthews coefficient Solvent content 3.16 61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.7 α = 90 b = 103.7 β = 101.3 c = 90.6 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 291 IMAGE PLATE MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR571
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.3 17 88.7 8.5 2 100992 2 15.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 82.9 5.7 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 PDB ENTRY 3SC2 2.3 8 2 50480 5122 85.2 0.165 0.165 0.164 0.222 0.163 RANDOM 18.9
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 x_dihedral_angle_d 25.1 x_scangle_it 6.32 x_scbond_it 4.42 x_mcangle_it 3.91 x_angle_deg 3.1 x_mcbond_it 2.61 x_improper_angle_d 1.21 x_bond_d 0.017 x_bond_d_na x_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 25.1 x_scangle_it 6.32 x_scbond_it 4.42 x_mcangle_it 3.91 x_angle_deg 3.1 x_mcbond_it 2.61 x_improper_angle_d 1.21 x_bond_d 0.017 x_bond_d_na x_bond_d_prot x_angle_d x_angle_d_na x_angle_d_prot x_angle_deg_na x_angle_deg_prot x_dihedral_angle_d_na x_dihedral_angle_d_prot x_improper_angle_d_na x_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6748 Nucleic Acid Atoms Solvent Atoms 331 Heterogen Atoms 146
Software Software Software Name Purpose X-PLOR refinement MOSFLM data reduction SCALEPACK data scaling X-PLOR phasing