3EXI | pdb_00003exi

Crystal structure of the pyruvate dehydrogenase (E1p) component of human pyruvate dehydrogenase complex with the subunit-binding domain (SBD) of E2p, but SBD cannot be modeled into the electron density

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	Mix the proteins with the ratio of E1p:SBD=1:2.10% PEG 6000, 1.5M NaCl, 0.1M BisTris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.63	66.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 154.378	α = 90
b = 154.378	β = 90
c = 82.949	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 315		2005-10-25	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	2.2	50	99.5	0.034	33	6.6		57582

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	2.2	2.24	95.5		0.558	2	6.5	2736

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	2.2	50	56609	1511	97.78	0.189	0.187	0.19	0.226	0.22	RANDOM	49.348

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]
-2.85	-1.42		-2.85		4.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.689
r_dihedral_angle_3_deg	16.634
r_dihedral_angle_4_deg	14.452
r_dihedral_angle_1_deg	6.356
r_scangle_it	4.695
r_scbond_it	2.98
r_angle_refined_deg	1.733
r_mcangle_it	1.588
r_mcbond_it	0.882
r_chiral_restr	0.116

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.689
r_dihedral_angle_3_deg	16.634
r_dihedral_angle_4_deg	14.452
r_dihedral_angle_1_deg	6.356
r_scangle_it	4.695
r_scbond_it	2.98
r_angle_refined_deg	1.733
r_mcangle_it	1.588
r_mcbond_it	0.882
r_chiral_restr	0.116
r_bond_refined_d	0.02
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5098
Nucleic Acid Atoms
Solvent Atoms	318
Heterogen Atoms	3

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
HKL-2000	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.