1X80

Crystal structure of the human mitochondrial branched-chain alpha-ketoacid dehydrogenase

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.8	293	PEG4000, pH 5.80, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.5	50

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 144.403	α = 90
b = 144.403	β = 90
c = 69.009	γ = 120

Symmetry
Space Group	P 31 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		2002-10-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID		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	50	96.2	0.074	19.4		53838	53838		-3

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	2.03	76		0.378

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1OLS	2	50	52347	52346	1479	96.22	0.16122	0.16122	0.16032	0.19252	RANDOM	34.334

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]
2.33	1.16		2.33		-3.49

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.908
r_dihedral_angle_4_deg	19.251
r_dihedral_angle_3_deg	15.487
r_dihedral_angle_1_deg	6.09
r_scangle_it	4.359
r_scbond_it	3.022
r_angle_refined_deg	1.775
r_mcangle_it	1.635
r_mcbond_it	1.007
r_nbtor_refined	0.326
r_nbd_refined	0.223
r_symmetry_hbond_refined	0.167
r_symmetry_vdw_refined	0.158
r_xyhbond_nbd_refined	0.153
r_chiral_restr	0.124
r_metal_ion_refined	0.088
r_bond_refined_d	0.02
r_gen_planes_refined	0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5514
Nucleic Acid Atoms
Solvent Atoms	391
Heterogen Atoms	36

Software

Software
Software Name	Purpose
HKL-2000	data collection
HKL-2000	data reduction
AMoRE	phasing
REFMAC	refinement
HKL-2000	data scaling