4NOG | pdb_00004nog

Crystal structure of a putative ornithine aminotransferase from Toxoplasma gondii ME49 in complex with pyrodoxal-5'-phosphate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3LG0	PDB ENTRY 3LG0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2 M Ammonium Acetate, 0.1 M Bis-Tris, 35% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.19	α = 100.58
b = 61.328	β = 93.23
c = 63.678	γ = 107.74

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 225 mm CCD	beryllium lenses	2013-10-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

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	1.2	62.14	91	0.043	11.2	2	224574	224574		-3	14.4

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	1.2	1.22	91		0.37	2	2	11241

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 (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 3LG0	1.2	62.14	213305	213305	11260	90.85	0.13481	0.13322	0.1324	0.16494	0.1651	RANDOM	18.365

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]
0.29	-0.59	0.58	0.01	1.34	-0.73

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.552
r_sphericity_bonded	27.542
r_rigid_bond_restr	25.184
r_sphericity_free	24.018
r_dihedral_angle_4_deg	17.237
r_dihedral_angle_3_deg	12.555
r_scangle_other	10.775
r_scbond_it	10.55
r_scbond_other	10.55
r_long_range_B_other	8.96
r_long_range_B_refined	8.777
r_dihedral_angle_1_deg	6.07
r_mcangle_other	5.581
r_mcangle_it	5.577
r_mcbond_it	4.662
r_mcbond_other	4.66
r_angle_refined_deg	1.927
r_angle_other_deg	0.966
r_chiral_restr	0.152
r_bond_refined_d	0.021
r_gen_planes_refined	0.011
r_bond_other_d	0.004
r_gen_planes_other	0.003
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6560
Nucleic Acid Atoms
Solvent Atoms	1041
Heterogen Atoms	65

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling