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Crystal structure of full-length, homohexameric 2-oxoglutarate dehydrogenase KGD from Mycobacterium smegmatis in complex with GarA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XT6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.1 M bicine pH 8.0, 30% (v/v) PEG550MME, 0.2 M NaCl
Crystal Properties Matthews coefficient Solvent content 4.09 69.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 325.75 α = 90 b = 325.75 β = 90 c = 396.944 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 315r 2008-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.9763 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 4.562 282.108 94.6 0.245 0.2565 0.0758 0.998 8.11 11.45 121219
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 4.562 4.778 52.9 1.9145 2.0014 0.5828 0.701 1.48 11.78 6059
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 4.562 45.99 121081 6055 89.6 0.1998 0.1983 0.1902 0.2292 0.2167 RANDOM 236.11
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] -5.1547 -5.1547 10.3094
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 2.83 t_omega_torsion 2.21 t_angle_deg 0.73 t_bond_d 0.006 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 56835 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 170
Software Software Software Name Purpose autoPROC data processing autoPROC data processing Aimless data scaling autoPROC data processing BUSTER refinement autoPROC data reduction PHASER phasing