1ZY8 | pdb_00001zy8

The crystal structure of dihydrolipoamide dehydrogenase and dihydrolipoamide dehydrogenase-binding protein (didomain) subcomplex of human pyruvate dehydrogenase complex.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3LAD	PDB entries: 3LAD and 1JEH
experimental model	PDB	1JEH	PDB entries: 3LAD and 1JEH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	295	PEG 6000, diammonium citrate, potassium phosphate buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.9	54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 168.79	α = 90
b = 186.91	β = 90
c = 217.54	γ = 90

Symmetry
Space Group	P 21 21 21

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 4		2003-04-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	1.1	NSLS	X25

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	2.59	50	88.4	0.164		3.3		188229

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)
	2.59	2.68	59.5		0.357		2

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	de novo chain building for E3-binding protein	THROUGHOUT	PDB entries: 3LAD and 1JEH	2.59	45.64	188162	158086	8336	88.45	0.275	0.275	0.208	0.2054	0.27592	0.2716	RANDOM	37.188

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]
-4.08			-1.18		5.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.099
r_scangle_it	2.814
r_mcangle_it	2.633
r_angle_refined_deg	2.116
r_scbond_it	1.705
r_mcbond_it	1.487
r_symmetry_vdw_refined	0.328
r_nbd_refined	0.3
r_xyhbond_nbd_refined	0.222
r_symmetry_hbond_refined	0.217
r_chiral_restr	0.116
r_bond_refined_d	0.03
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	36865
Nucleic Acid Atoms
Solvent Atoms	492
Heterogen Atoms	530

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing
CNS	refinement