3UPD | pdb_00003upd

2.9 Angstrom Crystal Structure of Ornithine Carbamoyltransferase (ArgF) from Vibrio vulnificus

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	295	Protein: 7.2mG/mL, 0.25M Sodium chloride, 0.01M Tris-HCl (pH 8.3); Screen: Calssics II (C2), 1.1M Ammonium tartrate (pH 7.0); Cryo: 4.0M Sodium formate, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.84	67.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 153.963	α = 90
b = 153.963	β = 90
c = 153.963	γ = 90

Symmetry
Space Group	I 21 3

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	Mirrors	2011-11-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.97903	APS	21-ID-D

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	2.9	30	100	0.095	18.3	6	13533	13533		-3	82.7

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	2.9	2.95	100		0.597	3.3	6	642

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	1DUV	2.91	28.11	12861	12861	669	99.98	0.15978	0.15978	0.15799	0.16	0.19452	0.19	RANDOM	58.788

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.981
r_dihedral_angle_4_deg	15.637
r_dihedral_angle_3_deg	10.731
r_scangle_it	4.376
r_scbond_it	2.747
r_dihedral_angle_1_deg	1.898
r_mcangle_it	1.731
r_angle_refined_deg	1.488
r_angle_other_deg	0.885
r_mcbond_it	0.882

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.981
r_dihedral_angle_4_deg	15.637
r_dihedral_angle_3_deg	10.731
r_scangle_it	4.376
r_scbond_it	2.747
r_dihedral_angle_1_deg	1.898
r_mcangle_it	1.731
r_angle_refined_deg	1.488
r_angle_other_deg	0.885
r_mcbond_it	0.882
r_mcbond_other	0.153
r_chiral_restr	0.094
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2698
Nucleic Acid Atoms
Solvent Atoms	47
Heterogen Atoms

Software

Software
Software Name	Purpose
Blu-Ice	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.