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Bacteroides ovatus mixed-linkage glucan utilization locus (MLGUL) SGBP-A with cellohexaose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6DK2 PDB entry 6DK2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 Molecular Dimensions Crystal Strategy Screen I, well G3 (0.2 M magnesium chloride, 0.1 M Tris acetate, pH 8.5, 25% PEG2000 MME).
Crystal Properties Matthews coefficient Solvent content 3.19 61.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 228.845 α = 90 b = 228.845 β = 90 c = 246.517 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 CCD MARMOSAIC 300 mm CCD 2016-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.979 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.4 49.6 99.93 0.2249 0.2396 0.996 8.4 8.5 283596
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.487 99.52 1.755 0.58 1.11 7.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 6DK2 2.4 49.6 269456 14140 99.87 0.1922 0.1896 0.1914 0.2423 0.2416 RANDOM 34.414
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] -1.49 -0.74 -1.49 4.83
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 70.055 r_dihedral_angle_2_deg 35.698 r_sphericity_bonded 31.192 r_dihedral_angle_4_deg 17.646 r_dihedral_angle_3_deg 15.77 r_dihedral_angle_1_deg 6.323 r_rigid_bond_restr 3.612 r_angle_refined_deg 0.996 r_angle_other_deg 0.812 r_chiral_restr 0.047
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 70.055 r_dihedral_angle_2_deg 35.698 r_sphericity_bonded 31.192 r_dihedral_angle_4_deg 17.646 r_dihedral_angle_3_deg 15.77 r_dihedral_angle_1_deg 6.323 r_rigid_bond_restr 3.612 r_angle_refined_deg 0.996 r_angle_other_deg 0.812 r_chiral_restr 0.047 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 40685 Nucleic Acid Atoms Solvent Atoms 944 Heterogen Atoms 812
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing PDB_EXTRACT data extraction