1DY8
Inhibition of the Hepatitis C Virus NS3/4A Protease. The Crystal Structures of Two Protease-Inhibitor Complexes (inhibitor II)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.1 | 277 | THE NS3 PROTEIN (1MG/ML) WAS INCUBATE AT 4C WITH THE NS4A COFACTOR PEPTIDE, CONTAINING A SOLUBIZING LYSINE TAG AT ITS N- AND C-TERMINI(KGSVVIVGRIILSGRK), AT A MOLAR RATIO OF 1:2 AND CONCENTRATED TO 290 MICROMOLAR. NS3J/4A CRYSTAL WITH A MAXIMUM SIZE OF 0.6 X 0.3 X 0.2 MM**3, WERE OBTAINED BY BOTH HANGING- AND SITTING-DROP VAPOUR DIFFUSION METHODS AFTER TW WEEKS AT ROOM TEMPERATURE, WITH 3.4 M NACL, 10MM DTT, 0.1 M CITR BUFFER PH 5.1. THE TERNARY COMPLEX WITH INHIBITOR WAS PREPARED B ADDING 2.5 MM OF INIBITOR TO CRYSTALS THAT WERE STABILISED IN 4.5 M NACL, 10 MM DTT, 0.1 M CITRATE BUFFER, PH 5.1., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.37 | 47.68 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 93.82 | α = 90 |
b = 93.82 | β = 90 |
c = 80.95 | γ = 120 |
Symmetry | |
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Space Group | P 61 |
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 | MARRESEARCH | BENT MIRROR | 1998-08-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE X31 | EMBL/DESY, HAMBURG | X31 |
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 | 2.4 | 20 | 99.8 | 0.137 | 4.7 | 3.5 | 15872 | -3 | 40.68 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.4 | 2.53 | 99.8 | 0.425 | 1.7 | 3.4 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1DY7 | 2.4 | 20 | 15872 | 788 | 99.8 | 0.216 | 0.221 | 0.318 | RANDOM | 45.4 |
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 |
p_transverse_tor | 29.3 |
p_staggered_tor | 21.4 |
p_scangle_it | 10.52 |
p_scbond_it | 10.1 |
p_planar_tor | 7.8 |
p_mcangle_it | 6.61 |
p_mcbond_it | 4.98 |
p_multtor_nbd | 0.284 |
p_xyhbond_nbd | 0.233 |
p_singtor_nbd | 0.21 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2734 |
Nucleic Acid Atoms | |
Solvent Atoms | 95 |
Heterogen Atoms | 74 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DENZO | data reduction |
SCALA | data scaling |
AMoRE | phasing |