5E3K

Crystal structure of the ornithine aminotransferase from Toxoplasma gondii ME49 in a complex with (S)-4-amino-5-fluoropentanoic acid

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4NOG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	0.2 M AmmSO4, 0.1 M Bis-Tris, 25% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.328	α = 100.72
b = 61.524	β = 92.96
c = 63.555	γ = 108.18

Symmetry
Space Group	P 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	MARMOSAIC 300 mm CCD		2015-02-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.97913	APS	21-ID-D

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	1.7	30	97.3	0.06	20.9	3		84366

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	1.7	1.73	95.7		0.5	1.9	2.4

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4NOG	1.7	30	80138	4228	96.41	0.1559	0.15374	0.19601	RANDOM	22.798

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]
-0.95	-1.64	-0.83	1.04	-0.5	1.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.945
r_dihedral_angle_4_deg	18.739
r_dihedral_angle_3_deg	12.598
r_dihedral_angle_1_deg	6.34
r_long_range_B_refined	5.467
r_long_range_B_other	5.467
r_scangle_other	1.807
r_angle_refined_deg	1.749
r_scbond_it	1.182
r_scbond_other	1.182
r_angle_other_deg	1.041
r_mcangle_it	1.039
r_mcangle_other	1.038
r_mcbond_it	0.672
r_mcbond_other	0.672
r_chiral_restr	0.108
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6560
Nucleic Acid Atoms
Solvent Atoms	813
Heterogen Atoms	114

Software

Software
Software Name	Purpose
BLU-MAX	data collection
HKL-3000	data scaling
PHASER	phasing
Coot	model building
REFMAC	refinement
HKL-3000	data reduction