2IHW | pdb_00002ihw

Crystal structure of a cubic core of the dihydrolipoamide acyltransferase (E2b) component in the branched-chain alpha-ketoacid dehydrogenase complex (BCKDC), apo form

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	292	0.1 M Na-acetate (pH 4.6), 28% PEG 4000, 0.15 M NH4-acetate, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2.73	54.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 194.654	α = 90
b = 194.654	β = 90
c = 171.93	γ = 120

Symmetry
Space Group	H 3

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		2005-12-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.98000	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	2.7	50	97.8	0.056	18.6	3		65296

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	2.7	2.8	94.5		0.474		2.6	6309

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB Entry 1EAA	2.7	50	65279	3301	97.65	0.186	0.183	0.2	0.257	0.26	RANDOM	54.357

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]
-2.62	-1.31		-2.62		3.93

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.272
r_dihedral_angle_3_deg	21.129
r_dihedral_angle_4_deg	18.121
r_dihedral_angle_1_deg	6.561
r_scangle_it	3.525
r_scbond_it	2.265
r_angle_refined_deg	1.89
r_mcangle_it	1.508
r_mcbond_it	0.877
r_nbtor_refined	0.325

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.272
r_dihedral_angle_3_deg	21.129
r_dihedral_angle_4_deg	18.121
r_dihedral_angle_1_deg	6.561
r_scangle_it	3.525
r_scbond_it	2.265
r_angle_refined_deg	1.89
r_mcangle_it	1.508
r_mcbond_it	0.877
r_nbtor_refined	0.325
r_nbd_refined	0.242
r_symmetry_vdw_refined	0.236
r_symmetry_hbond_refined	0.175
r_xyhbond_nbd_refined	0.159
r_chiral_restr	0.117
r_bond_refined_d	0.02
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14424
Nucleic Acid Atoms
Solvent Atoms	138
Heterogen Atoms	76

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

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.