1KI8 | pdb_00001ki8

CRYSTAL STRUCTURE OF THYMIDINE KINASE FROM HERPES SIMPLEX VIRUS TYPE I COMPLEXED WITH 5-BROMOVINYLDEOXYURIDINE

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5		HANGING-DROP: 8ML PROTEIN SOLUTION PLUS 4ML PRECIPITATING SOLUTION EQUILIBRATED AGAINST PRECIPITATING SOLUTION AT 25 C. PROTEIN SOLUTION: HSV-TK 1.0MG/ML; 40MM TRIS-CL PH 7.5; 3MM DTT; 0.2MM DT. PRECIPITATING SOLUTION: 30% SATURATED AMMONIUM SULPHATE; 200MM TRIS-CL PH 6.75; 3MM DTT; 0.2 MM DT. EXCHANGE OF DEOXYTHYMIDINE BOUND TO THE PROTEIN FOR 5-BROMOVINYLDEOXYURIDINE WAS MADE BY WASHING THE CRYSTALS FIVE TIMES IN A 3 ML SOLUTION (33% SATURATED AMMONIUM SULPHATE; 100MM TRIS-CL PH 6.75) CONTAINING 5-BROMOVINYLDEOXYURIDINE (BVDU)., vapor diffusion - hanging drop

Crystal Properties
Matthews coefficient	Solvent content
2.66	54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.4	α = 90
b = 116.9	β = 90
c = 108.2	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	120	IMAGE PLATE	RIGAKU RAXIS IIC	MIRRORS	1996-11-30	M

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.15		95	0.118		4		36243		-3	25.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.15	2.25	92		1.5	2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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	MIR + NCS IMPROVEMENT AND SOLVENT FLATTENING FOR ORIGINAL NATIVE, 1KIN	2.2	12	2.8	28510	2853	78	0.199	0.199	0.21	0.29	0.29	RANDOM	19

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
x_dihedral_angle_d	22.74
x_mcangle_it	2
x_scangle_it	2
x_angle_deg	1.921
x_improper_angle_d	1.724
x_mcbond_it	1.5
x_scbond_it	1.5
x_bond_d	0.011
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
x_angle_deg_prot
x_dihedral_angle_d_na
x_dihedral_angle_d_prot
x_improper_angle_d_na
x_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4676
Nucleic Acid Atoms
Solvent Atoms	249
Heterogen Atoms	48

Software

Software
Software Name	Purpose
SOLOMON	phasing
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling