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Venezuelan Equine Encephalitis Virus (VEEV) Nonstructural Protein 2 (nsP2) Cysteine Protease Inhibited with CA074
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 7 290 Modified JCSG+ Condition 8 (0.2 M Ammonium formate, 20% w/v PEG3350, 20% glycerol). Protein buffer contained 50 mM HEPES pH 7.0, 0.5 mM CA074, and 30 mM CaCl2
Crystal Properties Matthews coefficient Solvent content 2.18 43.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.762 α = 90 b = 63.582 β = 90 c = 86.283 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 150 CCD Bruker Platinum 135 2015-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR-H 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.32 63.58 94.6 0.1311 0.0508 18.03 13.35 14251
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.32 2.42 92.8 0.4357 0.1717 6.08 12.79
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.32 51.186 14184 678 94.478 0.191 0.1903 0.198 0.2003 0.2061 19.752
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] -1.602 0.72 0.882
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.257 r_dihedral_angle_4_deg 19.898 r_dihedral_angle_3_deg 16.127 r_dihedral_angle_1_deg 6.564 r_dihedral_angle_other_3_deg 4.958 r_lrange_it 4.284 r_lrange_other 4.257 r_mcangle_it 2.245 r_mcangle_other 2.245 r_scangle_it 2.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.257 r_dihedral_angle_4_deg 19.898 r_dihedral_angle_3_deg 16.127 r_dihedral_angle_1_deg 6.564 r_dihedral_angle_other_3_deg 4.958 r_lrange_it 4.284 r_lrange_other 4.257 r_mcangle_it 2.245 r_mcangle_other 2.245 r_scangle_it 2.13 r_scangle_other 2.129 r_angle_other_deg 1.358 r_mcbond_it 1.273 r_mcbond_other 1.272 r_scbond_it 1.255 r_scbond_other 1.255 r_angle_refined_deg 1.229 r_nbd_refined 0.193 r_symmetry_nbd_other 0.193 r_xyhbond_nbd_refined 0.171 r_nbd_other 0.17 r_nbtor_refined 0.164 r_symmetry_xyhbond_nbd_refined 0.142 r_symmetry_nbd_refined 0.133 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.06 r_symmetry_xyhbond_nbd_other 0.057 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2552 Nucleic Acid Atoms Solvent Atoms 135 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling PHASER phasing