2G25

E. Coli Pyruvate Dehydrogenase Phosphonolactylthiamin Diphosphate Complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1L8APDB ENTRY 1L8A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7291PEG2000 MONOMETHYL ETHER, PROPANOL, SODIUM AZIDE, HEPES BUFFER, MAGNESIUM CHLORIDE, PHOSPHONOLACTYL- THIAMIN DIPHOSPHATE, PH 7.00, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K
Crystal Properties
Matthews coefficientSolvent content
2.3447.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.57α = 90
b = 142.51β = 102.37
c = 82.09γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93AREA DETECTORSIEMENS HI-STAROsmic Mirrors2002-03-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

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
12.140.5940.0650.08724.824.79969999699
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.12.19605.51

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 1L8A2.18299699950524807940.2040.1850.1850.244RANDOM10.55
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]
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d24.87
x_scangle_it3.129
x_scbond_it2.166
x_mcangle_it1.698
x_angle_deg1.3
x_mcbond_it1.11
x_improper_angle_d0.72
x_bond_d0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13182
Nucleic Acid Atoms
Solvent Atoms564
Heterogen Atoms95

Software

Software
Software NamePurpose
X-GENdata scaling
FBSCALEdata reduction
PHASESphasing
X-PLORrefinement
FRAMBOdata collection
FBSCALEdata scaling