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Crystal structure of Paradendryphiella salina PL7C alginate lyase mutant H124 soaked with with tetra-mannuronic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8QIZ
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 1.97 37.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.54 α = 90 b = 38.77 β = 116.91 c = 75.17 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 EIGER2 X 9M 2020-09-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.976 ESRF ID30B
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 1.12 38.67 98.33 0.78 12.98 5.4 75488 7.65
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 1.12 1.15 0.7
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.12 38.67 1.36 75488 2099 98.31 0.1445 0.1439 0.1678 0.1794 12.02
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 13.1418 f_angle_d 1.079 f_chiral_restr 0.092 f_plane_restr 0.0086 f_bond_d 0.0068
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1728 Nucleic Acid Atoms Solvent Atoms 419 Heterogen Atoms 49
Software Software Software Name Purpose PHENIX refinement MxCuBE data collection XDS data reduction XDS data scaling Coot model building PHASER phasing