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Structure Determinants of Substrate Specificity of Hydroxynitrile Lyase from Manihot esculenta
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DWP PDB ENTRY 1DWP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.4 0.1 M NACITRAT, PH 5.4, 5% PEG8000, 28% MPD
Crystal Properties Matthews coefficient Solvent content 4.3 71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.34 α = 90 b = 106.34 β = 90 c = 188.84 γ = 90
Symmetry Space Group P 41 21 2
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 MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 EMBL/DESY, HAMBURG X11
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 2.1 20 99.4 0.052 19.2 6.5 63477 21.6
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 2.1 2.17 99.9 0.154 5.1 6.4
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1DWP 2.1 8 2 60760 6079 97.1 0.197 0.197 0.244 RANDOM 28.7
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 23.9 x_scangle_it 6.04 x_scbond_it 3.92 x_angle_deg 2.9 x_mcangle_it 2.77 x_mcbond_it 1.83 x_improper_angle_d 1.12 x_bond_d 0.015 x_bond_d_na x_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 23.9 x_scangle_it 6.04 x_scbond_it 3.92 x_angle_deg 2.9 x_mcangle_it 2.77 x_mcbond_it 1.83 x_improper_angle_d 1.12 x_bond_d 0.015 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 4160 Nucleic Acid Atoms Solvent Atoms 271 Heterogen Atoms 36
Software Software Software Name Purpose X-PLOR refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing