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Crystal structure of MERS-CoV N-NTD complexed with 5-Benzyloxygramine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4J3K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 5 mg/mL protein, 25 mM Tris-HCl, pH 7.5, 75 mM NaCl, 70 mM MES, pH5.5, 37.5 M (NH4)2SO4, 14.5 % PEG 3350, 1 mM NaBr, 1 mM 5-Benzyloxygramine
Crystal Properties Matthews coefficient Solvent content 2.73 54.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.489 α = 90 b = 108.477 β = 101.16 c = 91.595 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 IMAGE PLATE MAR scanner 300 mm plate 2015-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.90000 SPring-8 BL44XU
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 2.76 30 99.5 0.072 0.079 0.031 11.8 6.3 17388
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 2.77 2.87 99.4 0.477 0.514 0.19 0.922 7.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4J3K 2.77 29.394 1.41 17363 1742 99.05 0.2354 0.2315 0.2707 0.2267 RANDOM 35.3863
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 2.993 f_angle_d 1.339 f_chiral_restr 0.056 f_bond_d 0.008 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3549 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms 41
Software Software Software Name Purpose PHENIX refinement HKL-2000 data collection PHENIX phasing HKL-2000 data reduction HKL-2000 data scaling