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BoGH13ASus from Bacteroides ovatus bound to acarbose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8DGE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 10 mM acarbose, 0.1 M HEPES/MOPS, pH 7.5, 0.12 monosaccharides mix (Glc, Man, Gal, Fuc, Xyl, GlcNAc), 20% ethylene glycol, 10% PEG8000
Crystal Properties Matthews coefficient Solvent content 2.75 55.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.08 α = 90 b = 125.31 β = 102.11 c = 150.78 γ = 90
Symmetry Space Group P 1 21 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 9M 2019-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.078 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.99 38.6 98.5 0.086 0.997 9.6 4.7 244819
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 1.99 2.06 1.05 0.587
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 8DGE 1.99 38.6 232585 12246 98.48 0.1776 0.1754 0.1843 0.2188 0.2234 RANDOM 24.256
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] 0.06 -0.06 -0.09 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.899 r_dihedral_angle_4_deg 17.498 r_dihedral_angle_3_deg 14.194 r_dihedral_angle_1_deg 7.411 r_angle_refined_deg 1.613 r_angle_other_deg 1.345 r_chiral_restr 0.075 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.899 r_dihedral_angle_4_deg 17.498 r_dihedral_angle_3_deg 14.194 r_dihedral_angle_1_deg 7.411 r_angle_refined_deg 1.613 r_angle_other_deg 1.345 r_chiral_restr 0.075 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 22732 Nucleic Acid Atoms Solvent Atoms 2276 Heterogen Atoms 706
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction xia2 data reduction PHASER phasing