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Venezuelan Equine Encephalitis Virus (VEEV) Nonstructural Protein 2 (nsP2) Cysteine Protease Inhibited by E64d
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 7.6 290 JCSG+ Condition #8 (0.2 M Ammonium formate, 20% PEG 3350)
Crystal Properties Matthews coefficient Solvent content 2.32 43.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.89 α = 90 b = 63.63 β = 90 c = 86.75 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 2015-03-06 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 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 2.16 60.89 99.2 0.0591 14.16 7.3 18605 16
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 2.16 2.26 96.2 0.2655 4.91 4.04
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 2.16 51.31 17649 906 99.21 0.19161 0.18976 0.1971 0.22702 0.2356 RANDOM 17.415
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] -0.02 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.674 r_dihedral_angle_4_deg 14.477 r_dihedral_angle_3_deg 12.673 r_dihedral_angle_1_deg 6.293 r_angle_other_deg 3.703 r_long_range_B_refined 3.383 r_long_range_B_other 3.213 r_angle_refined_deg 1.383 r_mcangle_it 1.254 r_mcangle_other 1.254
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.674 r_dihedral_angle_4_deg 14.477 r_dihedral_angle_3_deg 12.673 r_dihedral_angle_1_deg 6.293 r_angle_other_deg 3.703 r_long_range_B_refined 3.383 r_long_range_B_other 3.213 r_angle_refined_deg 1.383 r_mcangle_it 1.254 r_mcangle_other 1.254 r_scangle_other 1.103 r_mcbond_it 0.687 r_mcbond_other 0.686 r_scbond_it 0.625 r_scbond_other 0.624 r_chiral_restr 0.099 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_gen_planes_other 0.005 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 2551 Nucleic Acid Atoms Solvent Atoms 208 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling PHASER phasing