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Resurrected Ancestral Hydroxynitrile Lyase from Flowering Plants
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YB6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 293 1:1 mix of protein (in 5mM BES buffer) with mother liquor (1.1 Molar Ammonium Citrate, 50 mM bis-tris propane, pH 6.8)
Crystals formed after 2-3 weeks at 20 degrees C.
Crystals were cryo-protected in 5% glycerol in mother liquor for 10 seconds then flash frozen in LN2.
Crystal Properties Matthews coefficient Solvent content 2.44 49.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.265 α = 90 b = 108.265 β = 90 c = 201.188 γ = 90
Symmetry Space Group P 43 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 MAR scanner 300 mm plate 2014-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.0332 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.96 29.32 99.3 0.097 0.998 13.8 8.5 86348
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.96 1.99 88.3 0.68 0.772 5.8
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 1YB6 1.96 29.32 81902 4319 99.28 0.1792 0.1767 0.1859 0.2265 0.2301 RANDOM 38.133
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] 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.483 r_dihedral_angle_3_deg 15.665 r_dihedral_angle_4_deg 14.161 r_dihedral_angle_1_deg 6.539 r_mcangle_it 2.789 r_angle_refined_deg 2.346 r_mcbond_it 1.991 r_mcbond_other 1.991 r_angle_other_deg 1.207 r_chiral_restr 0.165
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.483 r_dihedral_angle_3_deg 15.665 r_dihedral_angle_4_deg 14.161 r_dihedral_angle_1_deg 6.539 r_mcangle_it 2.789 r_angle_refined_deg 2.346 r_mcbond_it 1.991 r_mcbond_other 1.991 r_angle_other_deg 1.207 r_chiral_restr 0.165 r_bond_refined_d 0.027 r_gen_planes_refined 0.013 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8396 Nucleic Acid Atoms Solvent Atoms 192 Heterogen Atoms 36
Software Software Software Name Purpose Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data processing