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Crystal Structure of Rift Valley Fever Virus Nucleocapsid Protein Pentamer 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 28% PEG3350, 280 mM ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.81 56.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.81 α = 101.7 b = 93.59 β = 90.27 c = 124.78 γ = 114.18
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 3.9 121.596 99.1 0.212 2.8 2 28961 28961
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 3.9 4.11 99.1 0.463 0.463 1 2 4197
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3LYF 3.9 41.6 28958 1459 99.17 0.229 0.228 0.2484 0.3045 SHELL 55.482
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] 10.9485 7.4022 7.6542 -19.1423 17.4195 8.1938
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 3.19 t_omega_torsion 1.65 t_angle_deg 0.87 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 3.19 t_omega_torsion 1.65 t_angle_deg 0.87 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 19084 Nucleic Acid Atoms 1400 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose SCALA data scaling BUSTER-TNT refinement PDB_EXTRACT data extraction Blu-Ice data collection MOSFLM data reduction PHASER phasing BUSTER refinement