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Crystal structure of Bacteroides ovatus DhuD complexed with NAD+ responsible for metabolism of glycosaminoglycan
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CXR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 PEG 8000, 2-propanol, HEPES, sodium acetate
Crystal Properties Matthews coefficient Solvent content 2.03 39.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 161.943 α = 90 b = 126.911 β = 102.38 c = 71.657 γ = 90
Symmetry Space Group C 1 2 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 2022-07-30 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 3.1 48.69 98.9 0.071 0.086 0.998 11.5 3.08 25615
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 3.1 3.28 98.5 0.645 0.774 0.812 1.7 3.19
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 3.1 48.69 24329 1281 99.02 0.19773 0.19537 0.1984 0.24175 0.2399 RANDOM 103.291
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] 4.36 -3.54 4.2 -6.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.247 r_long_range_B_refined 11.583 r_long_range_B_other 11.582 r_mcangle_other 8.31 r_mcangle_it 8.309 r_scangle_other 8.05 r_dihedral_angle_1_deg 5.753 r_mcbond_it 5.155 r_mcbond_other 5.148 r_scbond_it 4.815
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.247 r_long_range_B_refined 11.583 r_long_range_B_other 11.582 r_mcangle_other 8.31 r_mcangle_it 8.309 r_scangle_other 8.05 r_dihedral_angle_1_deg 5.753 r_mcbond_it 5.155 r_mcbond_other 5.148 r_scbond_it 4.815 r_scbond_other 4.814 r_dihedral_angle_2_deg 3.738 r_angle_refined_deg 0.966 r_angle_other_deg 0.358 r_chiral_restr 0.045 r_bond_refined_d 0.003 r_gen_planes_refined 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 11592 Nucleic Acid Atoms Solvent Atoms 2 Heterogen Atoms 264
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing