2JGD | pdb_00002jgd

E. COLI 2-oxoglutarate dehydrogenase (E1o)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6		SITTING DROP: 1UL 12% PEG 4000, 50MM SOCIUM CITRATE PH5.6. 1UL 10MG/ML TE1O. RESERVOIR: 1UL 12% PEG 4000, 50MM SOCIUM CITRATE PH5.6., pH 5.60

Crystal Properties
Matthews coefficient	Solvent content
3.41	63.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 142.493	α = 90
b = 142.493	β = 90
c = 251.811	γ = 90

Symmetry
Space Group	P 41 21 2

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			2005-05-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4		ESRF	ID14-4

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	2.6	70	99.9	0.14	17.2	8.7		80455		2

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	2.6	2.69	99.8		0.87	3	8.6

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	SAD	THROUGHOUT	2.6	29.09	76341	4041	99.9	0.189	0.186	0.18	0.25	0.24	RANDOM	31.54

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]
					-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.348
r_dihedral_angle_4_deg	21.838
r_dihedral_angle_3_deg	19.587
r_scangle_it	16.373
r_scbond_it	15.484
r_mcangle_it	10.148
r_dihedral_angle_1_deg	9.894
r_mcbond_it	8.388
r_angle_refined_deg	1.079
r_nbtor_refined	0.333
r_symmetry_vdw_refined	0.3
r_nbd_refined	0.259
r_xyhbond_nbd_refined	0.234
r_symmetry_hbond_refined	0.224
r_chiral_restr	0.091
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
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_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12563
Nucleic Acid Atoms
Solvent Atoms	735
Heterogen Atoms	46

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing