4EP1 | pdb_00004ep1

Crystal structure of anabolic ornithine carbamoyltransferase from Bacillus anthracis

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	SwissModel		SwissModel-generated model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.3	289	Protein: 10 mg/ml in 10 mM Tris-HCl pH 8.3, 500 mM NaCl and 5 mM b-mercaptoethanol. Precipitant: 0.2M potassium sodium tartrate, 18% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
3.32	62.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 182.438	α = 90
b = 182.438	β = 90
c = 182.438	γ = 90

Symmetry
Space Group	P 41 3 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 315r	mirrors	2012-03-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97926	APS	19-ID

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	3.25	50	100	0.163	0.163	22.8	10.6		16913		-3	87.7

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	3.25	3.31	100		0.931	0.931	3.1	11.1	793

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	SwissModel-generated model	3.25	50	16102	16002	856	99.38	0.1724	0.1724	0.1704	0.1749	0.2091	0.2087	RANDOM	84.0478

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	39.46
r_dihedral_angle_4_deg	27.349
r_dihedral_angle_3_deg	16.535
r_dihedral_angle_1_deg	6.987
r_angle_refined_deg	1.629
r_angle_other_deg	1.127
r_chiral_restr	0.082
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d	0.004
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4591
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
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
Coot	model building