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X-ray structure of MERS coronavirus papain-like protease in complex with human ISG15
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4RF1 4RF1, 1Z2M experimental model PDB 1Z2M 4RF1, 1Z2M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.3 293.15 0.25 M Potassium Citrate, pH 8.3
20% PEG3350
Crystal Properties Matthews coefficient Solvent content 3.1 60.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 148.035 α = 90 b = 148.035 β = 90 c = 134.189 γ = 120
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 DECTRIS EIGER X 9M 2017-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.978 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.291 100 98.6 0.1 0.116 0.058 10.9 3.8 48452 30.81
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.291 2.34 99 0.56 0.657 0.337 0.732 3.6
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 4RF1, 1Z2M 2.291 42.734 1.99 48445 2006 98.32 0.1735 0.1715 0.1751 0.215 0.2171 45.2931
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 15.664 f_angle_d 1.065 f_chiral_restr 0.04 f_bond_d 0.013 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6354 Nucleic Acid Atoms Solvent Atoms 399 Heterogen Atoms 228
Software Software Software Name Purpose PHENIX refinement SCALEPACK data scaling PDB_EXTRACT data extraction HKL-3000 data reduction PHENIX phasing