3IT6 | pdb_00003it6

The Crystal Structure of Ornithine Acetyltransferase complexed with Ornithine from Mycobacterium tuberculosis (Rv1653) at 2.4 A

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1VZ6	PDB entry 1VZ6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	Protein concentration 13.5 mg/mL in 2.5 mM HEPES pH 7.5, Precipitant 0.02 M MgCl2, 22% polyacrylic acid 5100 in 0.1 M HEPES at pH 7.5, 3mM ornithine in mother liquor used to soak the crystal, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.89	57.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.849	α = 90
b = 100.095	β = 90
c = 156.401	γ = 90

Symmetry
Space Group	P 21 21 21

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	ADSC QUANTUM 315	Flat collimating mirror, double crystal monochromator, toroid focusing mirror	2008-11-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97946	SSRL	BL9-2

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	2.4	50	99.2	0.103	14.1	4.8	38018	38018

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	2.4	2.49	100		0.314	4.6	4.9	3755

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 1VZ6	2.4	50	35958	35958	1887	99.1	0.21241	0.20955	0.21	0.26695	0.27	RANDOM	30.093

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]
5.19			-2.53		-2.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.005
r_dihedral_angle_4_deg	16.322
r_dihedral_angle_3_deg	13.846
r_dihedral_angle_1_deg	5.704
r_scangle_it	2.171
r_scbond_it	1.275
r_angle_refined_deg	1.177
r_mcangle_it	0.811
r_mcbond_it	0.422
r_chiral_restr	0.074

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.005
r_dihedral_angle_4_deg	16.322
r_dihedral_angle_3_deg	13.846
r_dihedral_angle_1_deg	5.704
r_scangle_it	2.171
r_scbond_it	1.275
r_angle_refined_deg	1.177
r_mcangle_it	0.811
r_mcbond_it	0.422
r_chiral_restr	0.074
r_bond_refined_d	0.009
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5684
Nucleic Acid Atoms
Solvent Atoms	404
Heterogen Atoms	18

Software

Software
Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.