Experiment: 3TQZ

Structure of a deoxyuridine 5'-triphosphate nucleotidohydrolase (dut) from Coxiella burnetii

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	SITTING DROP	7.5	295	0.1 M HEPES, pH 7.5, 1.6 M ammonium sulfate, 0.1 M sodium chloride, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.45	64.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.065	α = 90
b = 85.065	β = 90
c = 54.76	γ = 120

Symmetry
Space Group	P 63

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	RIGAKU SATURN 944		2011-05-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

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	1.7	30	95.8	0.035	20.5	7.1	25001	23951		-3

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	1.7	1.73	60		0.373		1.5	742

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-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1DUD	1.75	19.523	24053	22549	1165	98.59	0.1758	0.1758	0.1752	0.1861	0.1866	RANDOM	29.194

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]
-0.0742			-0.0742		0.1483

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	12.687
f_angle_d	1.871
f_chiral_restr	0.157
f_bond_d	0.021
f_plane_restr	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1047
Nucleic Acid Atoms
Solvent Atoms	139
Heterogen Atoms	15

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling