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Inhibitor-bound structures of human pyruvate dehydrogenase kinase 4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y8N PDB ENTRY 1Y8N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.1 293 1.7M AMMONIUM SULFATE, 2% PEG 400, 0.1M SODIUM HEPES, 5% DMSO, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.22 44.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.083 α = 90 b = 69.081 β = 99.7 c = 85.627 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 RIGAKU JUPITER 210 2006-07-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32B2 1.00 SPring-8 BL32B2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.53 50 91.1 0.041 19.1 2.9 23666 35.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.53 2.62 94.1 0.326
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (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 1Y8N 2.54 48.68 23665 22738 1098 87 0.222 0.2204 0.29 0.2871 RANDOM 48.9
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] -3.34 -6.28 4.98 -1.65
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.8 c_scangle_it 2.74 c_mcangle_it 2.43 c_scbond_it 1.84 c_mcbond_it 1.43 c_angle_deg 0.9 c_improper_angle_d 0.67 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5495 Nucleic Acid Atoms Solvent Atoms 79 Heterogen Atoms 44
Software Software Software Name Purpose CNX refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing