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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 4PT5 PDB ENTRY 4PT5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 289 0.056 M sodium phosphate monobasic monohydrate, 1.344 M potassium phosphate, pH 8.0, 20% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.49 50.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.899 α = 90 b = 48.78 β = 121.52 c = 87.464 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 2014-10-09 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 1.794 19.731 98.7 0.079 0.079 6.714 5 33609 33172 1.27 41.6
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 1.794 1.89 94.1 1.348 0.6 4.8
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 PDB ENTRY 4PT5 1.794 19.731 31482 1681 98.94 0.1912 0.18853 0.192 0.2408 0.2455 RANDOM 41.631
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] -2.55 -1.67 3.51 -2.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.498 r_dihedral_angle_4_deg 24.939 r_dihedral_angle_3_deg 16.167 r_dihedral_angle_1_deg 6.489 r_angle_refined_deg 2.209 r_chiral_restr 0.136 r_bond_refined_d 0.019 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2504 Nucleic Acid Atoms Solvent Atoms 204 Heterogen Atoms 21
Software Software Software Name Purpose HKL-3000 data collection PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling