4JFR | pdb_00004jfr

Crystal structure of anabolic ornithine carbamoyltransferase from Vibrio vulnificus in complex with carbamoyl phosphate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4H31

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, 20 mM Carbamoyl phosphate, 500 mM NaCl and 5 mM b-mercaptoethanol. Crystallization condition: 0.1M Bis-Tris pH 6.5, 25% w/v PEG 3350, 0.2M Magnesium Chloride, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.46	49.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.343	α = 90
b = 80.916	β = 90
c = 177.637	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	2011-06-21		SINGLE WAVELENGT

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	2.17	50	99.6	0.072	0.072	35.1	6.3	62876	62625		-3	44.8

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	2.17	2.21	99.1		0.782	2	2	4.6	3070

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4H31	2.17	38.96	62834	62539	3172	99.53	0.1726	0.1726	0.1708	0.18	0.2054	0.21	RANDOM	58.1717

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]
-1.97			0.05		1.92

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.611
r_dihedral_angle_3_deg	15.932
r_dihedral_angle_4_deg	14.501
r_dihedral_angle_1_deg	5.887
r_angle_refined_deg	1.669
r_angle_other_deg	1.232
r_chiral_restr	0.095
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_bond_other_d	0.007

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.611
r_dihedral_angle_3_deg	15.932
r_dihedral_angle_4_deg	14.501
r_dihedral_angle_1_deg	5.887
r_angle_refined_deg	1.669
r_angle_other_deg	1.232
r_chiral_restr	0.095
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_bond_other_d	0.007
r_gen_planes_other	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7787
Nucleic Acid Atoms
Solvent Atoms	272
Heterogen Atoms	20

Software

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

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.