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1.83 Angstrom Resolution Crystal Structure of Dihydrolipoyl Dehydrogenase from Acinetobacter baumannii in Complex with FAD.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5U8U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 Protein: 22.6 mg/ml, 0.5M Sodium chloride, 0.01M Tris HCl (pH 8.3);
Screen: Classics II (G10), 0.2M Magnesium chloride, 0.1M Bis-Tris (pH 5.5), 25% (w/v) PEG 3350.
Crystal Properties Matthews coefficient Solvent content 2.08 40.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.965 α = 80.38 b = 82.769 β = 80.21 c = 96.262 γ = 89.49
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) 2017-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) 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 1.83 30 97.6 0.08 0.08 0.093 0.047 15.2 3.9 150403 -3 25.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.83 1.86 96.2 0.803 0.803 0.928 0.466 0.696 2.1 4
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 5U8U 1.83 29.63 142099 7557 97.6 0.18125 0.17903 0.1867 0.22202 0.2294 RANDOM 31.82
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] 0.18 1.07 0.2 1.89 -0.04 -1.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.745 r_dihedral_angle_4_deg 10.206 r_dihedral_angle_3_deg 9.84 r_long_range_B_refined 5.278 r_long_range_B_other 5.182 r_dihedral_angle_1_deg 3.103 r_scangle_other 2.712 r_mcangle_it 2.017 r_mcangle_other 2.017 r_scbond_it 1.679
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.745 r_dihedral_angle_4_deg 10.206 r_dihedral_angle_3_deg 9.84 r_long_range_B_refined 5.278 r_long_range_B_other 5.182 r_dihedral_angle_1_deg 3.103 r_scangle_other 2.712 r_mcangle_it 2.017 r_mcangle_other 2.017 r_scbond_it 1.679 r_scbond_other 1.678 r_angle_refined_deg 1.395 r_mcbond_it 1.227 r_mcbond_other 1.227 r_angle_other_deg 0.804 r_chiral_restr 0.083 r_gen_planes_refined 0.022 r_gen_planes_other 0.019 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 14064 Nucleic Acid Atoms Solvent Atoms 1234 Heterogen Atoms 225
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MoRDa phasing