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Crystal Structure of Rift Valley Fever Virus Nucleocapsid Protein Hexamer Bound to Single-stranded DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LYF PDB ENTRY 3LYF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 15% PEG3350, 350 mM sodium chloride, 100 mM Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.58 52.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.64 α = 90 b = 108.64 β = 90 c = 261.29 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 MARMOSAIC 300 mm CCD K-B pair of biomorph mirrors for vertical and horizontal focusing M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0332 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.7 94.085 99.6 0.114 10 4.4 25771 25771
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 2.7 2.85 98.5 0.779 0.779 1 4.3 3615
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 3LYF 2.7 53.66 25749 1313 99.29 0.1911 0.1891 0.1959 0.2299 0.2426 RANDOM 61.0411
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] -0.9209 -0.9209 1.8418
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 3.24 t_omega_torsion 2.49 t_angle_deg 1.06 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 3.24 t_omega_torsion 2.49 t_angle_deg 1.06 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5698 Nucleic Acid Atoms 277 Solvent Atoms 56 Heterogen Atoms
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing BUSTER-TNT refinement PDB_EXTRACT data extraction Blu-Ice data collection BUSTER refinement