3LQ4

E. coli pyruvate dehydrogenase complex E1 E235A mutant with high TDP concentration


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7298PEG2000 MONOMETHYL ETHER, PROPANOL,SODIUM AZIDE, HEPES BUFFER, MAGNESIUM CHLORIDE, THIAMIN DIPHOSPHATE, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.3848.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.21α = 90
b = 142.22β = 101.87
c = 82.85γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDMARMOSAIC 300 mm CCD2008-03-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.0APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.9832.52840.10622.152.711661110818020
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.982.185.40.3089.6217433

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONDIFFERENCE FOURIERTHROUGHOUT2IEA1.9832.52108180543383.70.1990.236RANDOM37.481
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]
-7.393.4-411.4
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d21.6
c_scangle_it3.181
c_mcangle_it2.131
c_scbond_it2.084
c_mcbond_it1.381
c_angle_deg1.2
c_improper_angle_d0.74
c_bond_d0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12674
Nucleic Acid Atoms
Solvent Atoms677
Heterogen Atoms79

Software

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