Experiment: 1WKL

Crystal Structure of Nucleoside Diphosphate Kinase from Thermus thermophilus HB8 in Complex with ATP and ADP

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	293	14% PEG4000, 0.09M Ammonium Acetate, 18% glycerol, 0.1M Sodium Citrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.8	67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 122.897	α = 90
b = 122.897	β = 90
c = 105.492	γ = 120

Symmetry
Space Group	P 63 2 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	RIGAKU JUPITER 210		2003-12-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	1.0	SPring-8	BL38B1

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	2.2	50	99.8	0.062	72.6	20.3		497844		-3	34.7

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	2.2	2.8	100		0.228	20

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-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1WKJ	2.2	50	24463	23548	2326	96.5	0.217	0.237	RANDOM	31.4

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]
-2.259	1.325		-2.259		4.518

RMS Deviations
Key	Refinement Restraint Deviation
c_angle_deg	1.3
c_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2158
Nucleic Acid Atoms
Solvent Atoms	89
Heterogen Atoms	63

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement