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Bacteroides ovatus mixed-linkage glucan utilization locus (MLGUL) SGBP-A in complex with mixed-linkage heptasaccharide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6DK2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 296 0.2M magnesium chloride, 0.1M HEPES, 25% (w/v) PEG3350
Crystal Properties Matthews coefficient Solvent content 2.68 54.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.826 α = 90 b = 92.943 β = 90 c = 155.253 γ = 90
Symmetry Space Group P 21 21 21
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 2017-07-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-3 0.979 SSRL BL9-3
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 2.51 50 98.6 0.997 14.61 6.49 43053
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 2.51 2.66 92.3 0.887 3.51 5.37
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6DK2 2.51 39.65 40942 2112 98.59 0.1754 0.1729 0.2228 0.1931 RANDOM 28.427
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] -0.59 2.03 -1.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.169 r_dihedral_angle_4_deg 18.881 r_dihedral_angle_3_deg 13.665 r_dihedral_angle_1_deg 6.074 r_mcangle_it 1.697 r_angle_other_deg 1.401 r_mcbond_it 0.999 r_mcbond_other 0.998 r_angle_refined_deg 0.958 r_chiral_restr 0.047
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.169 r_dihedral_angle_4_deg 18.881 r_dihedral_angle_3_deg 13.665 r_dihedral_angle_1_deg 6.074 r_mcangle_it 1.697 r_angle_other_deg 1.401 r_mcbond_it 0.999 r_mcbond_other 0.998 r_angle_refined_deg 0.958 r_chiral_restr 0.047 r_bond_refined_d 0.005 r_gen_planes_other 0.005 r_gen_planes_refined 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8175 Nucleic Acid Atoms Solvent Atoms 420 Heterogen Atoms 166
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Coot model building PHASER phasing XDS data scaling