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Structure of mycobacterial lipoamide dehydrogenase bound to a triazaspirodimethoxybenzoyl inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2A8X PDB entry 2A8X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291 200 microM Lpd, 300 microM 3II, 600 microM NADH, 100 mM Tris pH 8.5, 10 mM NaCl, 11% PEG 10000, 15% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.58 52.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.9 α = 90 b = 98.4 β = 90 c = 123.8 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV Osmic multilayer 2008-08-06 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 Merge 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 2.42 50 98.9 0.08 12.7 4.4 39590 39154 -1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.42 2.51 98 0.356 3.6 3805
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-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 2A8X 2.42 29.66 39110 1942 98.8 0.185 0.1887 0.242 0.1792 RANDOM 29.197
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] -2.04 5.74 -3.7
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 2.65 c_mcangle_it 1.83 c_scbond_it 1.83 c_mcbond_it 1.14
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6930 Nucleic Acid Atoms Solvent Atoms 751 Heterogen Atoms 192
Software Software Software Name Purpose CNS refinement SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection MOLREP phasing DENZO data reduction