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The Crystal Structure and Mechanism of Human Glutaryl-CoA Dehydrogenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SIQ PDB ENTRY 1SIQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 292 MES buffer, PEG5KMME, Ammonium Sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.88 56.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.722 α = 90 b = 116.722 β = 90 c = 128.034 γ = 120
Symmetry Space Group P 64 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 277 IMAGE PLATE RIGAKU RAXIS IIC Mirrors 2000-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 2.6 29.82 83.9 0.088 11.3 2.4 13764 13764 1 2 14.9
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 2.6 2.64 61 0.32 2.2 2.1 482
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-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 1SIQ 2.6 29.82 13764 13764 1105 83.8 0.187 0.187 0.1872 0.24 0.2421 RANDOM 20.5
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] 0.55 16.78 0.55 -1.1
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.1 c_scangle_it 6.03 c_scbond_it 4.02 c_mcangle_it 3.66 c_mcbond_it 2.38 c_angle_deg 1.2 c_improper_angle_d 0.79 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3011 Nucleic Acid Atoms Solvent Atoms 77 Heterogen Atoms 109
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling CNS phasing