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Crystal Structure of Rift Valley Fever Virus Nucleocapsid Protein Hexamer Bound to Single-stranded RNA.
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 293 24% PEG3350, 350 mM ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.23 44.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.66 α = 119.95 b = 173.33 β = 99.34 c = 172.9 γ = 90.12
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 3.4 149.472 94.7 0.19 4 1.9 117933 117933 2
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 3.4 3.58 92.3 0.513 0.513 1.3 1.9 16752
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 3.4 57.42 117932 5935 94.72 0.2254 0.2246 0.306 0.2399 0.3138 SHELL 70.4665
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] -19.8577 5.0466 -4.8864 14.5611 -5.0849 5.2966
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 2.88 t_omega_torsion 1.51 t_angle_deg 0.85 t_bond_d 0.008 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 2.88 t_omega_torsion 1.51 t_angle_deg 0.85 t_bond_d 0.008 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 33876 Nucleic Acid Atoms 2160 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling BUSTER-TNT refinement PDB_EXTRACT data extraction Blu-Ice data collection PHASER phasing BUSTER refinement