4KWT

Crystal structure of unliganded anabolic ornithine carbamoyltransferase from Vibrio vulnificus at 1.86 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	289	Protein: 10 mg/ml in 10 mM Tris-HCl pH 8.3, 60 mM Arginine, 500 mM NaCl and 5 mM b-mercaptoethanol. Crystallization condition: 0.1M Bis-Tris pH 6.5, 23% w/v PEG 3350, 0.2M Lithium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.81	α = 90
b = 82.65	β = 90
c = 150.908	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	MARMOSAIC 300 mm CCD	BE-LENSES	2012-06-21		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.86	50	98.3	0.075	0.075	35.1	5.6	82600	81196		-3	30.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.86	1.89	99.2		0.968	0.968	2.1	5.2	4055

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4H31	1.86	35.5	82448	81046	4051	98.3	0.1613	0.1613	0.1595	0.1952	RANDOM	39.7325

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]
-2.85			-0.77		3.62

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.212
r_dihedral_angle_4_deg	16.963
r_dihedral_angle_3_deg	14.396
r_dihedral_angle_1_deg	5.866
r_angle_refined_deg	1.738
r_angle_other_deg	1.382
r_chiral_restr	0.109
r_bond_refined_d	0.019
r_gen_planes_refined	0.011
r_bond_other_d	0.009

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.212
r_dihedral_angle_4_deg	16.963
r_dihedral_angle_3_deg	14.396
r_dihedral_angle_1_deg	5.866
r_angle_refined_deg	1.738
r_angle_other_deg	1.382
r_chiral_restr	0.109
r_bond_refined_d	0.019
r_gen_planes_refined	0.011
r_bond_other_d	0.009
r_gen_planes_other	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7515
Nucleic Acid Atoms
Solvent Atoms	487
Heterogen Atoms	11

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
CCP4	phasing
Coot	model building

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.