3EXF | pdb_00003exf

Crystal structure of the pyruvate dehydrogenase (E1p) component of human pyruvate dehydrogenase complex

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	12% PEG 8000, 140mM NaOAC, 50mM BisTris pH6.5, 10% glucose, 50mM Taurine, 8mM MgCl2, and 10mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.92	57.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.389	α = 90
b = 129.668	β = 109.15
c = 144.946	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	ADSC QUANTUM 315		2008-02-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.98	APS	19-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	2.998	50	99.8	0.146	10.699	3.7		72201

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.998	3.05	98.2		0.56		3.4	3543

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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		THROUGHOUT	2.998	50	72121	3624	99.37	0.189	0.185	0.1901	0.263	0.2659	RANDOM	21.411

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]
0.09		1.8	-3.18		4.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.919
r_dihedral_angle_3_deg	21.975
r_dihedral_angle_4_deg	20.649
r_dihedral_angle_1_deg	7.307
r_scangle_it	3.883
r_scbond_it	2.287
r_angle_refined_deg	2.025
r_mcangle_it	1.342
r_mcbond_it	0.664
r_chiral_restr	0.122

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.919
r_dihedral_angle_3_deg	21.975
r_dihedral_angle_4_deg	20.649
r_dihedral_angle_1_deg	7.307
r_scangle_it	3.883
r_scbond_it	2.287
r_angle_refined_deg	2.025
r_mcangle_it	1.342
r_mcbond_it	0.664
r_chiral_restr	0.122
r_bond_refined_d	0.02
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	21386
Nucleic Acid Atoms
Solvent Atoms	9
Heterogen Atoms	112

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
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.