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BoGH13ASus-E523Q from Bacteroides ovatus bound to maltoheptaose
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 12% MPD, 12% PEG1000, 12% PEG3350, 0.1M Tris/Bicine pH 8.5, 0.08M ethylene glycols mix
Crystal Properties Matthews coefficient Solvent content 2.75 55.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.68 α = 90 b = 128.64 β = 105.37 c = 149.76 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 2020-02-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.033 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 2.09 47.93 98.7 0.074 0.998 10 3.9 212239
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 2.09 2.17 1.12 0.467
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 2.09 47.93 201678 10581 98.75 0.179 0.1767 0.185 0.2226 0.2273 RANDOM 26.133
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] -0.17 -0.03 0.12 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.419 r_dihedral_angle_4_deg 17.377 r_dihedral_angle_3_deg 14.465 r_dihedral_angle_1_deg 7.473 r_angle_refined_deg 1.607 r_angle_other_deg 1.322 r_chiral_restr 0.088 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.419 r_dihedral_angle_4_deg 17.377 r_dihedral_angle_3_deg 14.465 r_dihedral_angle_1_deg 7.473 r_angle_refined_deg 1.607 r_angle_other_deg 1.322 r_chiral_restr 0.088 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 22685 Nucleic Acid Atoms Solvent Atoms 1887 Heterogen Atoms 955
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction xia2 data reduction PHASER phasing