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Bacteroides ovatus polysaccharide lyase family 38 (BoPL38) wild type in complex tetramannuronic acid at pH 8
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 HEPES pH 8
Crystal Properties Matthews coefficient Solvent content 3.02 59.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 197.327 α = 90 b = 89.355 β = 120.561 c = 146.509 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 2022-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.873128 ESRF ID23-2
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 2.11 79.08 99.9 0.996 6.7 6.7 124537 29.85
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 2.12 5.75 0.677
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 2.12 60.84 1.35 124507 6174 99.89 0.1786 0.1765 0.1764 0.219 0.2189 32.15
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 15.7988 f_angle_d 0.9467 f_chiral_restr 0.0526 f_plane_restr 0.0082 f_bond_d 0.0075
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12216 Nucleic Acid Atoms Solvent Atoms 888 Heterogen Atoms 196
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing