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Mutant L331A of deglycosylated hydroxynitrile lyase isozyme 5 from Prunus communis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6JBY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.25 289 Tris-bicine, 100 mM, pH 8.25; CaCl2, 60 mM; MgCl2, 60 mM; PEG 500MME, 24%, v/v; PEG 20000, 12%, w/v
Crystal Properties Matthews coefficient Solvent content 2.52 51.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.553 α = 90 b = 91.162 β = 90 c = 130.924 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS3 S 6M 2020-01-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.9789 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.595 50 98.8 0.086 0.089 0.025 8.5 12.1 78549
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 98.2 0.393 0.41 0.115 0.95 12.4
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6JBY 1.595 41.313 1.35 78405 4002 98.27 0.1536 0.1526 0.153 0.1735 0.1737 16.6967
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 f_dihedral_angle_d 7.879 f_angle_d 0.92 f_chiral_restr 0.055 f_bond_d 0.006 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3989 Nucleic Acid Atoms Solvent Atoms 760 Heterogen Atoms 165
Software Software Software Name Purpose HKL-3000 data scaling PHENIX refinement PDB_EXTRACT data extraction HKL-3000 data reduction PHENIX phasing