6V0T | pdb_00006v0t

Crystal Structure of Catalytic Subunit of Bovine Pyruvate Dehydrogenase Phosphatase 1 - Catalytic Domain

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1A6Q

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	7.5	298	The protein solution was 20mg/mL in 10 mM Tris-HCl, pH 7.3, 50 mM NaCl, 1mM MnSO4, 2mM DTT, and 1mM benzamide. The well solution (mixed 1:1) contained 0.10M HEPES, pH 7.5 and 20% Jeffamine M-600., Hanging drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.339	α = 90
b = 75.339	β = 90
c = 173.255	γ = 120

Symmetry
Space Group	P 32 2 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	ADSC QUANTUM 210		2002-07-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1	0.97900	ALS	8.2.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.1	52.117	96	0.085	35.3	4		33626

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.155			0.33

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1A6Q	2.1	52.117	1.33	33298	2784	97.73	0.221	0.2186	0.2466	45.2942

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]

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3046
Nucleic Acid Atoms
Solvent Atoms	226
Heterogen Atoms	15

Software

Software
Software Name	Purpose
HKL-2000	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
DENZO	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.