2QTA

E. coli Pyruvate dehydrogenase E1 component E401K mutant with thiamin diphosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2IEAPDB ENTRY 2IEA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.05295PEG 2000 monomethyl ether, proponal, sodium azide, hepes buffer, magnesium chloride, thiamin diphosphate, pH 7.05, Vapour diffusion, temperature 295K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties
Matthews coefficientSolvent content
2.3547.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.81α = 90
b = 141.83β = 102.01
c = 82.56γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2006-03-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.00APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.8538.0698.70.0740.07427.926.815523915193114.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.9294.20.3360.3367.7614769

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONDIFFERENCE FOURIERTHROUGHOUTPDB ENTRY 2IEA1.8538.06151931151931768597.10.2250.2250.2140.237RANDOM20.6
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]
-0.522.15-2.943.46
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23
c_angle_deg1.4
c_improper_angle_d1.01
c_mcangle_it0.48
c_scangle_it0.365
c_mcbond_it0.257
c_scbond_it0.21
c_bond_d0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12682
Nucleic Acid Atoms
Solvent Atoms413
Heterogen Atoms54

Software

Software
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
MAR345data collection
HKL-2000data reduction
SCALEPACKdata scaling