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Structure of MK-3281, a Potent Non-Nucleoside Finger-Loop Inhibitor, in complex with the Hepatitis C Virus NS5B Polymerase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CSJ PDB ENTRY 1CSJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 277 SOAKING WITH COMPOUND MK3281 WAS PERFORMED AT 4 DEG C BY TRANSFERRING THE APO-NS5B CRYSTALS FOR 10 MIN IN A SOLUTION CONTAINING 100 MM 2-MORPHOLINOETHANESULFONIC ACID (MES), PH 6.0, 14% POLYETHYLENE GLYCOL (PEG) 8,000, 14% 2- PROPANOL, 2.5 MM TCEP, 10 MM MNCL2 AND 2.5 MM OF COMPOUND MK3281. THE CRYSTALS WERE THEN TRANSFERRED FOR 1 MIN TO A CRYO-PROTECTANT SOLUTION CONTAINING 100 MM MES PH 6.0, 14% POLYETHYLENE GLYCOL PEG 8,000, 14% 2-PROPANOL, 18% 2-METHYL-2,5 PENTANEDIOL (MPD), 2.5 MM TCEP, 5 MM MNCL2 AND 1.25 MM COMPOUND MK3281 AND THEN PLUNGED DIRECTLY INTO LIQUID NITROGEN.
Crystal Properties Matthews coefficient Solvent content 2.6 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.983 α = 90 b = 94.272 β = 90 c = 95.145 γ = 90
Symmetry Space Group P 21 21 2
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 ADSC QUANTUM 210 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
Data Collection Overall 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 2.53 20 99.7 0.09 5.9 3.9 20692 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.53 2.67 99.7 0.53 1.5 3.8
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 1CSJ 2.53 95.35 19605 1056 99.63 0.23727 0.23332 0.2303 0.31016 0.3011 RANDOM 54.851
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] 1.15 -5.32 4.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.962 r_dihedral_angle_3_deg 18.535 r_dihedral_angle_4_deg 17.26 r_dihedral_angle_1_deg 5.734 r_scangle_it 2.504 r_scbond_it 1.543 r_angle_refined_deg 1.349 r_mcangle_it 0.916 r_mcbond_it 0.468 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.962 r_dihedral_angle_3_deg 18.535 r_dihedral_angle_4_deg 17.26 r_dihedral_angle_1_deg 5.734 r_scangle_it 2.504 r_scbond_it 1.543 r_angle_refined_deg 1.349 r_mcangle_it 0.916 r_mcbond_it 0.468 r_chiral_restr 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3911 Nucleic Acid Atoms Solvent Atoms 130 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing