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Crystal structure of PLpro from Middle East Respiratory Syndrome (MERS) coronavirus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FE8 PDB ENTRY 2FE8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 289 1.0 M sodium citrate, 0.1 M cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.5 50.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.82 α = 90 b = 47.26 β = 121.6 c = 88.77 γ = 90
Symmetry Space Group C 1 2 1
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 MARMOSAIC 225 mm CCD 2013-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 2.59 19.88 93.7 0.078 0.106 8.8 2.8 11246 11005 -3 -3 58.5
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 2.59 2.74 92.1 1.06 1.44 1.05 2.8 1611
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2FE8 2.59 19.88 -3 -3 10484 10484 521 97.58 0.23197 0.23197 0.22859 0.29949 0.2799 RANDOM 76.955
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] -0.39 -0.14 0.52 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.741 r_dihedral_angle_3_deg 14.768 r_dihedral_angle_4_deg 13.708 r_dihedral_angle_1_deg 4.281 r_angle_refined_deg 0.872 r_chiral_restr 0.055 r_bond_refined_d 0.005 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2502 Nucleic Acid Atoms Solvent Atoms 23 Heterogen Atoms 1
Software Software Software Name Purpose iMOSFLM data reduction PHASER phasing REFMAC refinement XDS data reduction XDS data scaling