1E2J

The nucleoside binding site of Herpes simplex type 1 thymidine kinase analyzed by X-ray crystallography

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		LITHIUM SULPHATE, HEPES, DTT, DT, pH 7.50

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.4	α = 90
b = 117.5	β = 90
c = 108.6	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	AREA DETECTOR	MULTIWIRE SIEMENS		1998-11-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH2R

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	2.5	20	92	0.063	0.063	11.5	2.4		23273			28.3

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	2.5	2.64	92		0.17	0.17	3.1	1.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1VTK	2.5	20	23273	1164	91	0.212	0.273	RANDOM	28.4

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]

RMS Deviations
Key	Refinement Restraint Deviation
p_angle_d	0.022
p_bond_d	0.009
p_angle_deg
p_planar_d
p_hb_or_metal_coord
p_mcbond_it
p_mcangle_it
p_scbond_it
p_scangle_it
p_plane_restr
p_chiral_restr
p_singtor_nbd
p_multtor_nbd
p_xhyhbond_nbd
p_xyhbond_nbd
p_planar_tor
p_staggered_tor
p_orthonormal_tor
p_transverse_tor
p_special_tor

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4729
Nucleic Acid Atoms
Solvent Atoms	111
Heterogen Atoms	44

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
AMoRE	phasing