Experiment: 3ASY

ligand-free structure of uridine kinase from thermus thermophilus HB8

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1UEJ	uridine cytidine kinase2 from Homo sapiens

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	293	40% (v/v) isopropanol, 15%(w/v) PEG 8000, 0.1M imidazole, pH 6.5, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.364	α = 90
b = 70.364	β = 90
c = 179.243	γ = 90

Symmetry
Space Group	P 43 21 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	MARMOSAIC 225 mm CCD		2008-01-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B2	1.000	SPring-8	BL26B2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.4	50				18465	18465

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	2.4	2.49			0.64	6.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (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	uridine cytidine kinase2 from Homo sapiens	2.4	37.8	18465	18465	1715		0.233	0.2452	0.2995	0.2456	random	47.0139

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]
-4.483			-4.483		8.966

RMS Deviations
Key	Refinement Restraint Deviation
c_scangle_it	10.56
c_scbond_it	8.452
c_mcangle_it	7.396
c_mcbond_it	5.72

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3186
Nucleic Acid Atoms
Solvent Atoms	82
Heterogen Atoms

Software

Software
Software Name	Purpose
HKL-2000	data collection
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing