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Structure of a Self-inhibited N475A variant of the Venezuelan Equine Encephalitis Virus (VEEV) nsP2 cysteine protease
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HWK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 290 0.1 M Bicine pH 8.5, 20% PEG 6000, 10% glycerol
Crystal Properties Matthews coefficient Solvent content 2.14 42.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.527 α = 78.28 b = 45.528 β = 65.31 c = 47.765 γ = 88.81
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL Bruker PHOTON II HELIOS MX 2017-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER IMUS MICROFOCUS 1.54
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 2.08 44.46 97.4 0.0808 9.73 3.29 18603 3 20.1
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 2.08 2.18 97 0.3371 3.01 2.56
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 2HWK 2.1 44.46 15941 877 90.58 0.19797 0.19543 0.2038 0.24305 0.2475 RANDOM 22.945
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] -0.03 0.01 -0.01 -0.02 -0.01 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.692 r_dihedral_angle_4_deg 15.959 r_dihedral_angle_3_deg 11.969 r_dihedral_angle_1_deg 5.532 r_long_range_B_refined 4.618 r_long_range_B_other 4.593 r_angle_other_deg 3.629 r_scangle_other 2.928 r_mcangle_other 2.201 r_mcangle_it 2.199
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.692 r_dihedral_angle_4_deg 15.959 r_dihedral_angle_3_deg 11.969 r_dihedral_angle_1_deg 5.532 r_long_range_B_refined 4.618 r_long_range_B_other 4.593 r_angle_other_deg 3.629 r_scangle_other 2.928 r_mcangle_other 2.201 r_mcangle_it 2.199 r_scbond_it 1.847 r_scbond_other 1.846 r_angle_refined_deg 1.427 r_mcbond_it 1.427 r_mcbond_other 1.421 r_chiral_restr 0.082 r_bond_refined_d 0.012 r_gen_planes_other 0.01 r_gen_planes_refined 0.006 r_bond_other_d 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 2560 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling PHASER phasing