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Crystal structure of EV-D68 2A protease
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7LW2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 0.05 M Sodium Cacodylate pH 6.0,
0.005 M Magnesium Chloride,
0.002 M Calcium Chloride,
15% v/v 2-Propanol,
0.001 M Spermine
Crystal Properties Matthews coefficient Solvent content 2.96 58.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.157 α = 90 b = 118.157 β = 90 c = 81.735 γ = 90
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 315r 2020-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 1.0000 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 3.2 47.88 99.92 0.988 25.4 3.9 14387
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2 3.66 0.477
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7LW2 3.5 47.88 261.21 14387 1446 99.99 0.2432 0.2376 0.2346 0.2851 0.2826 117.15
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.0028 f_angle_d 0.7072 f_chiral_restr 0.0511 f_plane_restr 0.0053 f_bond_d 0.0032
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5980 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms 6
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing