4EU1 | pdb_00004eu1

Structure of a mitochondrial aspartate aminotransferase from Trypanosoma brucei

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4EFF	PDB entry 4EFF modified with CCP4 program chainsaw

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	290	EmeraldBio Wizard classic 3/4 B7: 20% PEG 3350, 200mM ammonium nitrate, TrbrA.34891.a.A1 PW34891 at 27.7 mg/ml, tray 232857g1, pH 7.5, vapor diffusion, sitting drop, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.51	51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.26	α = 90
b = 96.25	β = 111.62
c = 81.32	γ = 90

Symmetry
Space Group	P 1 21 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	RIGAKU SATURN 944+		2012-04-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.5418

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	2.3	50	98	0.085	12.82	3.8	39748	38947		-3	35.39

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	2.3	2.36	96.5		0.532	3.1	3.8

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 4EFF modified with CCP4 program chainsaw	2.3	50	38947	1963	98.14	0.1984	0.196	0.194	0.2447	0.2407	RANDOM	29.3858

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]
0.54		0.26	0.16		-0.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.461
r_dihedral_angle_4_deg	20.332
r_dihedral_angle_3_deg	14.467
r_dihedral_angle_1_deg	5.654
r_angle_refined_deg	1.375
r_angle_other_deg	1.081
r_chiral_restr	0.077
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.004
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5844
Nucleic Acid Atoms
Solvent Atoms	364
Heterogen Atoms	17

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
JDirector	data collection
XDS	data reduction