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Inhibition of the Hepatitis C Virus NS3/4A Protease. The Crystal Structures of Two Protease-Inhibitor Complexes (inhibitor I)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DY7 PDB ENTRY 1DY7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.1 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 CRYSTALS, 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 TWO WEEKS AT ROOM TEMPERATURE, WITH 3.4 M NACL, 10MM DTT, 0.1 M CITRATE BUFFER PH 5.1. THE TERNARY COMPLEX WITH INHIBITOR WAS PREPARED BY ADDING 5.0 MM OF INIBITOR TO CRYSTALS THAT WERE STABILISED IN 4.5 M NACL, 10 MM DTT, 0.1 M CITRATE BUFFER, PH 5.1.
Crystal Properties Matthews coefficient Solvent content 2.37 47.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.35 α = 90 b = 94.35 β = 90 c = 82.37 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARRESEARCH TOROIDAL MIRROR 1999-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 ESRF ID14-3
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 2.1 20 98.2 0.035 32 2.8 23960 -3 37.4
Highest Resolution Shell 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 2.1 2.14 98.4 0.15 3.2 2.1
Refinement Statistics 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 (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1DY7 2.1 20 23960 1224 98.2 0.207 0.213 0.275 0.2032 RANDOM 43.5
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 p_transverse_tor 26.4 p_staggered_tor 20.5 p_planar_tor 6.7 p_scangle_it 5.49 p_mcangle_it 4.18 p_scbond_it 3.77 p_mcbond_it 2.9 p_multtor_nbd 0.278 p_xyhbond_nbd 0.201 p_singtor_nbd 0.193
RMS Deviations Key Refinement Restraint Deviation p_transverse_tor 26.4 p_staggered_tor 20.5 p_planar_tor 6.7 p_scangle_it 5.49 p_mcangle_it 4.18 p_scbond_it 3.77 p_mcbond_it 2.9 p_multtor_nbd 0.278 p_xyhbond_nbd 0.201 p_singtor_nbd 0.193 p_chiral_restr 0.125 p_angle_d 0.03 p_planar_d 0.03 p_plane_restr 0.012 p_bond_d 0.01 p_angle_deg p_hb_or_metal_coord p_xhyhbond_nbd p_orthonormal_tor p_special_tor
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2734 Nucleic Acid Atoms Solvent Atoms 213 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing