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Crystal structure of Paradendryphiella salina PL7C alginate lyase mutant Y220F
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8BJR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 2 M Ammonium sulfate; 0.1 Sodium acetate pH 4.6
Crystal Properties Matthews coefficient Solvent content 2.03 39.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.973 α = 74.231 b = 39.971 β = 77.124 c = 42.636 γ = 69.814
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 EIGER X 16M 2020-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.9786 MAX IV BioMAX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.2 20.31 91.28 0.99 9.31 3.5 57526 10.17
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.24 0.75
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FREE R-VALUE 1.2 20.31 1.96 57276 2888 91.31 0.1402 0.1387 0.1387 0.168 0.169 15.62
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 12.9966 f_angle_d 0.9679 f_chiral_restr 0.0884 f_plane_restr 0.0077 f_bond_d 0.0067
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1737 Nucleic Acid Atoms Solvent Atoms 339 Heterogen Atoms 19
Software Software Software Name Purpose MxCuBE data collection PHENIX refinement autoPROC data processing XDS data scaling Coot model building PHASER phasing