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Crystal Structure of the Manihot esculenta Hydroxynitrile Lyase (MeHNL) 3KP (K176P, K199P, K224P) triple mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DWP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 25%(v/v) PEG 3350, 0.1M Tris/HCl (pH 8.5), 0.2M Ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.06 40.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.04 α = 90 b = 84.21 β = 90.2 c = 134.9 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 IMAGE PLATE RIGAKU RAXIS VII 2010-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E DW 1.5418
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 2.88 100 98.3 41899
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 2.9 3 97.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1DWP 2.88 15.26 41899 39489 2100 95.86 0.20597 0.20597 0.20427 0.2075 0.23785 0.2371 RANDOM 23.037
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] 0.06 -0.11 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.566 r_dihedral_angle_3_deg 19.869 r_dihedral_angle_4_deg 14.743 r_dihedral_angle_1_deg 6.376 r_angle_refined_deg 1.506 r_angle_other_deg 1.44 r_chiral_restr 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.566 r_dihedral_angle_3_deg 19.869 r_dihedral_angle_4_deg 14.743 r_dihedral_angle_1_deg 6.376 r_angle_refined_deg 1.506 r_angle_other_deg 1.44 r_chiral_restr 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.007 r_gen_planes_other 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16544 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction MOLREP phasing REFMAC refinement SCALEPACK data scaling