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Structural and Functional Characterization of the Novel Endo-alpha(1,4)-Fucoidanase Mef1 from the Marine Bacterium Muricauda eckloniae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6M8N 6M8N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 293 24 % PEG 3350, 0.1 M CAPSO pH 9, 3 % isopropanol, 4 % PEG 400
Crystal Properties Matthews coefficient Solvent content 2.78 55.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.416 α = 90 b = 105.416 β = 90 c = 78.247 γ = 120
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 PILATUS 6M 2020-10-24 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) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.8 43.72 99.87 0.1267 0.1369 0.05163 0.996 6.8 6.8 45842 25.27
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 1.8 1.864 99.6 1 1 0.4176 0.833 0.48
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 FREE R-VALUE 6M8N 1.8 43.72 1.35 45795 2259 99.88 0.1667 0.1648 0.1658 0.2016 0.2034 29.58
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 15.6436 f_angle_d 1.0717 f_chiral_restr 0.0582 f_bond_d 0.0103 f_plane_restr 0.0087
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2954 Nucleic Acid Atoms Solvent Atoms 355 Heterogen Atoms 55
Software Software Software Name Purpose PHENIX refinement xia2 data reduction DIALS data scaling PHASER phasing