2QTA | pdb_00002qta

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

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2IEA	PDB ENTRY 2IEA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.05	295	PEG 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 coefficient	Solvent content
2.35	47.67

Crystal Data

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

Symmetry
Space Group	P 1 21 1

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	MARMOSAIC 300 mm CCD		2006-03-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.00	APS	22-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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.85	38.06	98.7	0.074	0.074	27.92	6.8	155239	151931			14.4

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)	Redundancy	Number Unique Reflections (All)
1	1.85	1.92	94.2		0.336	0.336	7.7	6	14769

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	DIFFERENCE FOURIER	THROUGHOUT	PDB ENTRY 2IEA	1.85	38.06	151931	151931	7685	97.1	0.225	0.225	0.214	0.2	0.237	0.23	RANDOM	20.6

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]
-0.52		2.15	-2.94		3.46

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	23
c_angle_deg	1.4
c_improper_angle_d	1.01
c_mcangle_it	0.48
c_scangle_it	0.365
c_mcbond_it	0.257
c_scbond_it	0.21
c_bond_d	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12682
Nucleic Acid Atoms
Solvent Atoms	413
Heterogen Atoms	54

Software

Software
Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
HKL-2000	data reduction
SCALEPACK	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.