1KI6
CRYSTAL STRUCTURE OF THYMIDINE KINASE FROM HERPES SIMPLEX VIRUS TYPE I COMPLEXED WITH A 5-IODOURACIL ANHYDROHEXITOL NUCLEOSIDE
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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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. THE EXCHANGE OF DEOXYTHYMIDINE BOUND TO THE PROTEIN FOR THE ANHYDROUS HEXITOL NUCLEOSIDE WAS MADE BY WASHING THE CRYSTALS FIVE TIMES IN A 3 ML SOLUTION (33% SATURATED AMMONIUM SULPHATE; 100MM TRIS-CL PH 6.75) CONTAINING THE COMPOUND., vapor diffusion - hanging drop |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.2 | 44.1 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 113.6 | α = 90 |
b = 116.4 | β = 90 |
c = 108.4 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
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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 | 1996-09-16 | M |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 |
Data Collection
Overall | |||||||||||||||||||
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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 | 2.37 | 96 | 0.119 | 4 | 26808 | -3 | 23.5 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
2.37 | 2.48 | 96 | 4 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MIR + NCS IMPROVEMENT AND SOLVENT FLATTENING FOR ORIGINAL NATIVE, 1KIN | THROUGHOUT | 2.37 | 12 | 2 | 25870 | 2539 | 88 | 0.223 | 0.223 | 0.317 | RANDOM |
Temperature Factor Modeling | ||||||
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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 | |
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Key | Refinement Restraint Deviation |
x_dihedral_angle_d | 22.68 |
x_mcangle_it | 2 |
x_scangle_it | 2 |
x_angle_deg | 1.942 |
x_improper_angle_d | 1.562 |
x_mcbond_it | 1.5 |
x_scbond_it | 1.5 |
x_bond_d | 0.015 |
x_bond_d_na | |
x_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4627 |
Nucleic Acid Atoms | |
Solvent Atoms | 275 |
Heterogen Atoms | 46 |
Software
Software | |
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Software Name | Purpose |
SOLOMON | phasing |
X-PLOR | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |