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The crystal structure of the C-terminal domain of Ebola (Bundibugyo) nucleoprotein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4QB0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 Crystallization solution: 1.33 M LiSO4, 0.1 M Tris pH 8.5. 1:1 ratio (250 nL: 250 nL) of precipitant to protein (at a concentration of 13.9 mg/ml). 60 mcL reservoir. Protein purification buffer 50mM Tris-HCl, 150 mM NaCl; pH 7.5
Crystal Properties Matthews coefficient Solvent content 5.94 79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.957 α = 90 b = 108.957 β = 90 c = 82.736 γ = 120
Symmetry Space Group P 64 2 2
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 RAYONIX MX300HE 2014-08-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.99 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.3 80 94.3 0.084 20.3 14.8 12398
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 2.3 2.38 64.7 0.432 0.432 1.9 7.1
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 4QB0 2.31 80 11792 604 94.04 0.1692 0.1676 0.176 0.2025 0.2144 RANDOM 81.78
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] 0.68 0.34 0.68 -2.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.102 r_mcangle_it 14.363 r_mcbond_it 13.696 r_mcbond_other 13.629 r_dihedral_angle_3_deg 13.36 r_dihedral_angle_4_deg 10.807 r_dihedral_angle_1_deg 5.678 r_angle_refined_deg 1.253 r_angle_other_deg 0.899 r_chiral_restr 0.071
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.102 r_mcangle_it 14.363 r_mcbond_it 13.696 r_mcbond_other 13.629 r_dihedral_angle_3_deg 13.36 r_dihedral_angle_4_deg 10.807 r_dihedral_angle_1_deg 5.678 r_angle_refined_deg 1.253 r_angle_other_deg 0.899 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 861 Nucleic Acid Atoms Solvent Atoms 113 Heterogen Atoms 13
Software Software Software Name Purpose PDB_EXTRACT data extraction REFMAC refinement SBC-Collect data collection HKL-3000 phasing SCALEPACK data scaling PHENIX model building HKL-3000 data reduction Coot model building