2G28 | pdb_00002g28

E. Coli Pyruvate Dehydrogenase H407A variant Phosphonolactylthiamin Diphosphate Complex

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1L8A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.05	291	PEG2000 MONOMETHYL ETHER, PROPANOL, SODIUM AZIDE, HEPES BUFFER, MAGNESIUM CHLORIDE, PHOSPHONOLACTYL- THIAMIN DIPHOSPHATE, PH 7.00, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K, pH 7.05

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.99	α = 90
b = 143.2	β = 102.61
c = 82.53	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 225 mm CCD		2004-08-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.00013	APS	22-ID

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	1.55	41.77	79.4	0.076	12.26	3.2	237104	213020			16.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.55	1.67	32.8		1.46

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	1L8A	1.85	41.77	157076	150327	7535	95.2	0.227	0.216	0.216	0.21	0.24	0.24	RANDOM	21.1

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]
-1.81		0.48	0.79		1.02

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	22.9
c_angle_deg	1.5
c_improper_angle_d	0.94
c_mcangle_it	0.469
c_scangle_it	0.411
c_mcbond_it	0.255
c_scbond_it	0.246
c_bond_d	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12682
Nucleic Acid Atoms
Solvent Atoms	549
Heterogen Atoms	70

Software

Software
Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
PHASES	phasing
CNS	refinement
HKL-2000	data reduction

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.