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Crystal structure of Bacteroides ovatus KduI1 responsible for metabolism of glycosaminoglycan
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YWK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 PEG 10000, glycerol, TRIS, sodium chloride
Crystal Properties Matthews coefficient Solvent content 2.38 48.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.121 α = 90 b = 99.372 β = 119.72 c = 102.279 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 R 4M 2021-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.0 SPring-8 BL26B1
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 1.89 45.6 94.3 0.051 0.062 0.998 11.75 2.91 264658
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.89 2 76.3 0.68 0.843 0.657 2.44
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.89 45.6 129290 6805 95.85 0.19495 0.19343 0.2 0.22416 0.2301 RANDOM 36.176
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] -1.28 -0.77 4.06 -1.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.762 r_dihedral_angle_1_deg 6.749 r_long_range_B_refined 4.949 r_long_range_B_other 4.947 r_dihedral_angle_2_deg 4.162 r_scangle_other 3.408 r_mcangle_it 2.75 r_mcangle_other 2.75 r_scbond_it 2.12 r_scbond_other 2.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.762 r_dihedral_angle_1_deg 6.749 r_long_range_B_refined 4.949 r_long_range_B_other 4.947 r_dihedral_angle_2_deg 4.162 r_scangle_other 3.408 r_mcangle_it 2.75 r_mcangle_other 2.75 r_scbond_it 2.12 r_scbond_other 2.12 r_mcbond_it 1.793 r_mcbond_other 1.793 r_angle_refined_deg 1.061 r_angle_other_deg 0.408 r_chiral_restr 0.054 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12183 Nucleic Acid Atoms Solvent Atoms 450 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction MOLREP phasing