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Bacteroides ovatus polysaccharide lyase family 38 (BoPL38) mutant Y298F in complex tetramannuronic acid at pH 3.5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8BDQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 3.5 294.15 18% (W/V) PEG3350, 0.2 M (NH4)2SO4 and 0.1 M citric acid pH 3.5
soaked in tetramannuronic acid in 18% (W/V) PEG3350, 0.2 M (NH4)2SO4 and 0.1 M citric acid pH 3.5
Crystal Properties Matthews coefficient Solvent content 3.01 59.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 196.678 α = 90 b = 88.869 β = 120.177 c = 145.089 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 2022-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.97242 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 2.37 48.36 98.94 0.992 7.75 3.2 87072 49.21
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 2.37 2.4 0.494
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 2.37 48.36 1.36 87033 4286 98.94 0.1771 0.1752 0.1752 0.2138 0.2138 52.18
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 17.2885 f_angle_d 0.9837 f_chiral_restr 0.05 f_bond_d 0.0079 f_plane_restr 0.0075
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12204 Nucleic Acid Atoms Solvent Atoms 418 Heterogen Atoms 216
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing