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Crystal structure of Paradendryphiella salina PL7C alginate lyase mutant H124
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8C3X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 30% PEG3350, 0.1M Bis-Tris pH 5.5, 0.2M NaCl
Crystal Properties Matthews coefficient Solvent content 1.91 35.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.52 α = 90 b = 38.45 β = 116.62 c = 74.01 γ = 90
Symmetry Space Group C 1 2 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 PIXEL DECTRIS EIGER X 16M 2020-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.6525 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 0.98 33.52 98.64 1 17.36 6.8 213697 11.89
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 0.98 1 0.53
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 0.98 33.52 1.04 213697 2223 98.63 0.1239 0.1237 0.1238 0.1486 0.1491 18.83
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 13.9583 f_angle_d 1.1502 f_chiral_restr 0.1019 f_plane_restr 0.0102 f_bond_d 0.0064
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1746 Nucleic Acid Atoms Solvent Atoms 347 Heterogen Atoms 8
Software Software Software Name Purpose MxCuBE data collection PHENIX refinement XDS data reduction Coot model building PHASER phasing