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Bacteroides ovatus polysaccharide lyase family 38 (BoPL38) wild type in complex tetraguluronic 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 294.15 18% (W/V) PEG3350, 0.2 M (NH4)2SO4 and 0.1 M citric acid pH 3.5
soaked in tetraguluronic 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 59.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 196.935 α = 90 b = 89.034 β = 120.362 c = 145.908 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 2022-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.97625 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 2.54 62.95 99.65 0.982 6.56 7 71977 61.02
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 2.54 2.57 0.26
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 2.54 62.95 1.36 71746 3652 99.65 0.2073 0.2052 0.2055 0.2484 0.2487 64.65
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 15.708 f_angle_d 1.0872 f_chiral_restr 0.0551 f_bond_d 0.0089 f_plane_restr 0.0084
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12202 Nucleic Acid Atoms Solvent Atoms 332 Heterogen Atoms 211
Software Software Software Name Purpose PHENIX refinement xia2 data reduction xia2 data scaling PHASER phasing