3CVK
Crystal structure of HCV NS5B polymerase with a novel pyridazinone inhibitor
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.6 | 298 | 20% PEG 4K, 50 MM AMMONIUM SULFATE, 100 MM SODIUM ACETATE, 5 MM DTT, PH 4.7, TRANSFERED TO PH 7.6 FOR LIGAND SOAKING, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.25 | 45.3 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 86.302 | α = 90 |
b = 106.258 | β = 90 |
c = 126.225 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 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 | 100 | IMAGE PLATE | RIGAKU RAXIS IV | MIRRORS | 2006-10-31 | M | MAD |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RUH3R | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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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 | 2.31 | 38.12 | 99.9 | 0.21 | 5.15 | 4.1 | 51042 | 51042 | 37.7 |
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) | ||||||||||||
2.31 | 2.39 | 96.5 | 3.4 | 4910 |
Refinement
Statistics | |||||||||||||||||||
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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-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | HCV NS5B POLYMERASE | 2.31 | 38.12 | 51041 | 2606 | 98.95 | 0.2103 | 0.2103 | 0.20695 | 0.27228 | RANDOM | 47.778 |
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] | |
-1.11 | 2.42 | -1.31 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.836 |
r_dihedral_angle_3_deg | 15.301 |
r_dihedral_angle_4_deg | 15 |
r_dihedral_angle_1_deg | 5.543 |
r_scangle_it | 2.425 |
r_mcangle_it | 1.898 |
r_scbond_it | 1.701 |
r_mcbond_it | 1.184 |
r_angle_refined_deg | 1.155 |
r_nbtor_refined | 0.293 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8668 |
Nucleic Acid Atoms | |
Solvent Atoms | 278 |
Heterogen Atoms | 68 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
CrystalClear | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
EPMR | phasing |