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Crystal structure of the catalytic core of the 2-oxoacid dehydrogenase multienzyme complex from Thermoplasma acidophilum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EAF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 291 15% MPD, 0.2M NaCl, 0.1M Na Acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 5 75.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 204.84 α = 90 b = 204.84 β = 90 c = 441.94 γ = 120
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 ADSC QUANTUM 315 2010-05-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9702 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 4.01 44.95 100 29696 28168
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 4 4.14 100
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 (All) 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 1EAF 4.01 44.95 28168 1504 100 0.25672 0.25672 0.25291 0.2456 0.32773 0.3177 RANDOM 97.108
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] 0.01 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.137 r_dihedral_angle_3_deg 25.989 r_dihedral_angle_4_deg 21.106 r_dihedral_angle_1_deg 9.256 r_angle_refined_deg 1.806 r_scangle_it 1.303 r_scbond_it 0.73 r_mcangle_it 0.514 r_mcbond_it 0.263 r_chiral_restr 0.131
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.137 r_dihedral_angle_3_deg 25.989 r_dihedral_angle_4_deg 21.106 r_dihedral_angle_1_deg 9.256 r_angle_refined_deg 1.806 r_scangle_it 1.303 r_scbond_it 0.73 r_mcangle_it 0.514 r_mcbond_it 0.263 r_chiral_restr 0.131 r_bond_refined_d 0.015 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12157 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose ADSC data collection BALBES phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling