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1.72 Angstrom Resolution Crystal Structure of 2-Oxoglutarate Dehydrogenase Complex Subunit Dihydrolipoamide Dehydrogenase from Bordetella pertussis in Complex with FAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5U8U PDB entry 5U8U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 Protein in 0.3 M sodium chloride, 0.01 M HEPES, pH 7.5 against screen (0.2 M calcium acetate, 20% w/v PEG3350)
Crystal Properties Matthews coefficient Solvent content 2.21 44.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.801 α = 90 b = 68.801 β = 90 c = 199.396 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD C(111) 2017-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rpim I (All) 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 1.72 30 97.7 0.086 0.086 0.041 14.7 5 96213 -3 20.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.72 1.75 96.7 0.781 0.781 0.378 0.648 2 5
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 PDB entry 5U8U 1.72 29.92 90615 4844 97.67 0.17133 0.1695 0.1791 0.20529 0.2143 RANDOM 23.261
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] 0.51 0.51 -1.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.461 r_dihedral_angle_4_deg 10.65 r_dihedral_angle_3_deg 9.828 r_long_range_B_refined 5.27 r_long_range_B_other 4.861 r_dihedral_angle_1_deg 2.803 r_scangle_other 1.854 r_angle_refined_deg 1.42 r_mcangle_it 1.207 r_mcangle_other 1.207
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.461 r_dihedral_angle_4_deg 10.65 r_dihedral_angle_3_deg 9.828 r_long_range_B_refined 5.27 r_long_range_B_other 4.861 r_dihedral_angle_1_deg 2.803 r_scangle_other 1.854 r_angle_refined_deg 1.42 r_mcangle_it 1.207 r_mcangle_other 1.207 r_scbond_it 1.166 r_scbond_other 1.166 r_angle_other_deg 0.848 r_mcbond_it 0.74 r_mcbond_other 0.739 r_chiral_restr 0.083 r_gen_planes_refined 0.023 r_gen_planes_other 0.02 r_bond_refined_d 0.008 r_bond_other_d 0.001 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 7026 Nucleic Acid Atoms Solvent Atoms 1084 Heterogen Atoms 107
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MoRDa phasing