4ZLV | pdb_00004zlv

Crystal structure of the ornithine aminotransferase from Toxoplasma gondii ME49 in a complex with the Schiff base between PLP and Lys286

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	294	0.2 M AmmSO4, 0.1 M Bis-Tris, 25% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.481	α = 100.45
b = 61.459	β = 92.39
c = 63.435	γ = 108.32

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		2015-03-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.97889	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	1.8	30	96	0.03	22.1	1.8	70729	70729

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	1.8	1.83	87.4		0.46	1.5	1.7

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	4NGO	1.8	30	67239	3490	95.69	0.16408	0.16191	0.1698	0.20591	0.2131	RANDOM	35.798

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]
0.01	-2.64	-0.62	1.29	-0.53	0.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.109
r_dihedral_angle_4_deg	17.303
r_dihedral_angle_3_deg	13.143
r_dihedral_angle_1_deg	6.321
r_long_range_B_refined	5.727
r_long_range_B_other	5.675
r_scangle_other	1.716
r_angle_refined_deg	1.628
r_mcangle_it	1.225
r_mcangle_other	1.225
r_scbond_it	1.131
r_scbond_other	1.123
r_angle_other_deg	1
r_mcbond_it	0.757
r_mcbond_other	0.757
r_chiral_restr	0.095
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
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	6533
Nucleic Acid Atoms
Solvent Atoms	503
Heterogen Atoms	67

Software

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