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Structure of coxsackievirus B3 3C protease in complex with the alpha-ketoamide (S)-N-benzyl-3-((S)-2-cinnamamido-3-phenylpropanamido)-2-oxo-4-((S)-2-oxopyrrolidin-3-yl)butanamide (cinnamoyl-phenylalanine-GlnLactam-CO-CO-NH-benzyl)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Ccoxsackievirus B3 3C protease
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.1 M Tris-HCl, 0.2 M MgCl2, pH 8.5, and PEG 3350 varied from 22% to 27%
Crystal Properties Matthews coefficient Solvent content 2.18 43.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.657 α = 90 b = 64.354 β = 115.44 c = 39.477 γ = 90
Symmetry Space Group C 1 2 1
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 RAYONIX MX-225 2012-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.91841 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 1.8 47.41 99.4 0.034 0.023 0.999 18.9 3.1 16209
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 99.2 0.393 0.265 0.887 3
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 Ccoxsackievirus B3 3C protease 1.8 47.41 15381 828 99.3 0.1817 0.17867 0.1902 0.23933 0.2526 RANDOM 45.438
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] 0.35 1.94 -2.76 0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.988 r_dihedral_angle_4_deg 21.652 r_dihedral_angle_3_deg 13.602 r_dihedral_angle_1_deg 6.688 r_long_range_B_refined 6.401 r_long_range_B_other 6.399 r_scangle_other 3.461 r_mcangle_it 2.345 r_mcangle_other 2.343 r_scbond_it 2.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.988 r_dihedral_angle_4_deg 21.652 r_dihedral_angle_3_deg 13.602 r_dihedral_angle_1_deg 6.688 r_long_range_B_refined 6.401 r_long_range_B_other 6.399 r_scangle_other 3.461 r_mcangle_it 2.345 r_mcangle_other 2.343 r_scbond_it 2.298 r_scbond_other 2.297 r_angle_refined_deg 1.928 r_mcbond_it 1.677 r_mcbond_other 1.664 r_angle_other_deg 1.033 r_chiral_restr 0.111 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1398 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement SCALA data scaling MOLREP phasing