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2.3 Angstrom Resolution Crystal Structure of Dihydrolipoamide Dehydrogenase from Burkholderia cenocepacia in Complex with FAD and NAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LVL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 295 Protein: 8.0 mg/ml, 0.5 Sodium chloride, 0.01M Tris pH 8.3, 1mM FAD;
Screen: PACT (D1), 0.1M MMT buffer pH 4.0, 25% (w/v) PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.33 47.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.565 α = 90 b = 107.246 β = 106.09 c = 105.427 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 CCD MARMOSAIC 300 mm CCD C(111) 2018-02-06 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 2.3 30 100 0.109 0.109 0.124 0.059 13.2 4.4 79190 -3 42.9
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 2.3 2.34 100 0.791 0.791 0.909 0.443 0.624 1.9 4.1
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 1LVL 2.3 29.21 75207 3962 99.72 0.20144 0.19868 0.2005 0.2532 0.2543 RANDOM 50.659
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] -1.2 1.03 0.44 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.935 r_dihedral_angle_4_deg 12.459 r_dihedral_angle_3_deg 9.891 r_long_range_B_refined 5.389 r_long_range_B_other 5.37 r_scangle_other 3.031 r_mcangle_it 2.43 r_mcangle_other 2.43 r_dihedral_angle_1_deg 2.077 r_scbond_it 1.855
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.935 r_dihedral_angle_4_deg 12.459 r_dihedral_angle_3_deg 9.891 r_long_range_B_refined 5.389 r_long_range_B_other 5.37 r_scangle_other 3.031 r_mcangle_it 2.43 r_mcangle_other 2.43 r_dihedral_angle_1_deg 2.077 r_scbond_it 1.855 r_scbond_other 1.855 r_angle_refined_deg 1.466 r_mcbond_it 1.458 r_mcbond_other 1.458 r_angle_other_deg 0.891 r_chiral_restr 0.082 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 13576 Nucleic Acid Atoms Solvent Atoms 360 Heterogen Atoms 432
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MoRDa phasing