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Rat branched chain ketoacid dehydrogenase kinase in complex with inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4E00
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 16% PEG-3350 and 8% tacsimate pH 6.0 (Hampton Research). Fully grown crystals were soaked overnight in a solution of 8% tacsimate pH 6.0, 25% PEG-3350, 50 mM KCl, 50 mM MgCl2, 2 mM ADP, 20% glycerol, 5% DMSO, and 1.5 mM 6 (PF-07328948) and flash frozen in liquid nitrogen
Crystal Properties Matthews coefficient Solvent content 3.37 63.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.35 α = 90 b = 126.35 β = 90 c = 74.68 γ = 90
Symmetry Space Group P 42 21 2
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 X 16M 2020-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim 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 2.155 89.35 86.8 0.103 0.03 0.999 15.6 13.2 26167
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.155 2.292 46 2.728 0.761 0.439 1.1 13.5
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 2.155 25.27 26142 1327 78.8 0.2074 0.2059 0.1895 0.2357 0.2208 RANDOM 58.18
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] -1.4241 -1.4241 2.8481
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.94 t_omega_torsion 2.77 t_angle_deg 0.84 t_bond_d 0.007 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2526 Nucleic Acid Atoms Solvent Atoms 130 Heterogen Atoms 58
Software Software Software Name Purpose BUSTER refinement XDS data reduction STARANISO data scaling BUSTER phasing