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Crystal structure of Paradendryphiella salina PL7C alginate lyase soaked with dimannuronic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8PC3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 30% PEG3350, 0.1M Bis-Tris pH 5.5, 0.3M NaCl
Crystal Properties Matthews coefficient Solvent content 2.18 43.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.71 α = 90 b = 59.9 β = 90 c = 88.96 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 EIGER X 16M 2020-08-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.799 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 1.09 44.88 98.4 1 7.77 7.16 92201 13.33
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 1.09 1.16 0.46
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 1.09 37.77 1.35 92189 2101 98.35 0.1497 0.1491 0.1487 0.1774 0.1764 18.07
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 13.2598 f_angle_d 0.9536 f_chiral_restr 0.081 f_plane_restr 0.008 f_bond_d 0.0062
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1768 Nucleic Acid Atoms Solvent Atoms 306 Heterogen Atoms 50
Software Software Software Name Purpose MxCuBE data collection PHENIX refinement XDS data reduction XDS data scaling Coot model building PHASER phasing