1KI4

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


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5HANGING-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-BROMOTHIENYLDEOXYURIDINE 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-BROMOTHIENYLDEOXYURIDINE (BTDU)., vapor diffusion - hanging drop
Crystal Properties
Matthews coefficientSolvent content
1.2351.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.1α = 90
b = 116β = 90
c = 108.7γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120IMAGE PLATERIGAKU RAXIS IICMIRRORS1996-08-09M
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.341000.144429537-324.07
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.342.521004.54

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMIR + NCS IMPROVEMENT AND SOLVENT FLATTENING FOR ORIGINAL NATIVE, 1KINTHROUGHOUT2.34121.2253272515830.210.210.309RANDOM
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
KeyRefinement Restraint Deviation
x_dihedral_angle_d22.77
x_angle_deg2.016
x_mcangle_it2
x_scangle_it2
x_improper_angle_d1.616
x_mcbond_it1.5
x_scbond_it1.5
x_bond_d0.013
x_bond_d_na
x_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d22.77
x_angle_deg2.016
x_mcangle_it2
x_scangle_it2
x_improper_angle_d1.616
x_mcbond_it1.5
x_scbond_it1.5
x_bond_d0.013
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 AtomsNumber
Protein Atoms4627
Nucleic Acid Atoms
Solvent Atoms263
Heterogen Atoms54

Software

Software
Software NamePurpose
RAVEmodel building
SOLOMONphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
RAVEphasing