2I6U

Crystal Structure of Ornithine Carbamoyltransferase complexed with Carbamoyl Phosphate and L-Norvaline from Mycobacterium tuberculosis (Rv1656) at 2.2 A

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1FB5	PDB ENTRY 1FB5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	273	1.6M Magnesium Sulfate, 0.1M Bis-Tris, 8% PEG 400, 3% ethanol, 3mM L-Norvaline, 3mM Carbamoyl phosphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 273K

Crystal Properties
Matthews coefficient	Solvent content
3.31	62.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.149	α = 90
b = 99.149	β = 90
c = 463	γ = 120

Symmetry
Space Group	P 65 2 2

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	Vertical focusing mirror; single crystal Si(311) bent monochromator (horizontal focusing)	2006-07-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-1	0.979462	SSRL	BL9-1

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	2.2	49.568	73.8	0.082	16.4	5.5	69827	51538			24.1

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)
	2.2	2.28	43.9		0.307	3.3	3.1	2981

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1FB5	2.2	49.568	51719	48946	2592	73.81	0.17879	0.17561	0.23887	RANDOM	19.994

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]
-1.14	-0.57		-1.14		1.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.212
r_dihedral_angle_4_deg	18.548
r_dihedral_angle_3_deg	16.276
r_dihedral_angle_1_deg	6.265
r_scangle_it	4.03
r_scbond_it	2.503
r_angle_refined_deg	1.659
r_mcangle_it	1.5
r_mcbond_it	0.883
r_nbtor_refined	0.312

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.212
r_dihedral_angle_4_deg	18.548
r_dihedral_angle_3_deg	16.276
r_dihedral_angle_1_deg	6.265
r_scangle_it	4.03
r_scbond_it	2.503
r_angle_refined_deg	1.659
r_mcangle_it	1.5
r_mcbond_it	0.883
r_nbtor_refined	0.312
r_nbd_refined	0.208
r_xyhbond_nbd_refined	0.196
r_symmetry_hbond_refined	0.183
r_symmetry_vdw_refined	0.174
r_chiral_restr	0.117
r_bond_refined_d	0.016
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6978
Nucleic Acid Atoms
Solvent Atoms	572
Heterogen Atoms	73

Software

Software
Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing

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.