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Inhibition of the Hepatitis C Virus NS3/4A Protease. The Crystal Structures of Two Protease-Inhibitor Complexes (apo structure)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JXP PDB ENTRY 1JXP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.1 THE NS3 PROTEIN (1MG/ML) WAS INCUBATED 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.
Crystal Properties Matthews coefficient Solvent content 2.37 47.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.98 α = 90 b = 92.98 β = 90 c = 81.81 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 IMAGE PLATE MARRESEARCH BENT MIRROR 1999-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 EMBL/DESY, HAMBURG X11
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 2.4 20 100 0.071 9 8 15786 -3 45.57
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 2.4 2.53 99.9 0.36 2.2 5.6
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1JXP 2.4 20 15786 789 100 0.196 0.198 0.1806 0.298 0.1868 RANDOM 46.78
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 25 p_staggered_tor 21.6 p_scangle_it 13.97 p_scbond_it 12.14 p_planar_tor 9 p_mcangle_it 7.44 p_mcbond_it 5.57 p_multtor_nbd 0.3 p_xyhbond_nbd 0.24 p_singtor_nbd 0.22
RMS Deviations Key Refinement Restraint Deviation p_transverse_tor 25 p_staggered_tor 21.6 p_scangle_it 13.97 p_scbond_it 12.14 p_planar_tor 9 p_mcangle_it 7.44 p_mcbond_it 5.57 p_multtor_nbd 0.3 p_xyhbond_nbd 0.24 p_singtor_nbd 0.22 p_chiral_restr 0.14 p_planar_d 0.039 p_angle_d 0.037 p_plane_restr 0.014 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 209 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALA data scaling AMoRE phasing