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CryoEM structure of the Nipah virus nucleocapsid single helical turn assembly
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4CO6
Refinement RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 64.403 r_mcangle_it 41.647 r_scbond_it 37.599 r_dihedral_angle_2_deg 30.494 r_mcbond_it 28.042 r_dihedral_angle_4_deg 24.31 r_dihedral_angle_3_deg 15.904 r_dihedral_angle_1_deg 7.786 r_angle_refined_deg 2.213 r_chiral_restr 0.165
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 64.403 r_mcangle_it 41.647 r_scbond_it 37.599 r_dihedral_angle_2_deg 30.494 r_mcbond_it 28.042 r_dihedral_angle_4_deg 24.31 r_dihedral_angle_3_deg 15.904 r_dihedral_angle_1_deg 7.786 r_angle_refined_deg 2.213 r_chiral_restr 0.165 r_gen_planes_refined 0.014 r_bond_refined_d 0.012 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Sample Nipah virus nucleocapsid Protein-RNA complex Sample Components Nucleoprotein RNA (78-MER)
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 124891 Reported Resolution (Å) 3.5 Resolution Method FSC 0.143 CUT-OFF Other Details Local symmetry was applied using the reconstruction Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (4CO6) Refinement Space Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 41
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 500 Maximum Defocus (nm) 2100 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION RELION 3.0 IMAGE ACQUISITION EPU CTF CORRECTION CTFFIND 4 MODEL FITTING UCSF Chimera 1.13 CLASSIFICATION RELION 3.1beta RECONSTRUCTION RELION 3.1beta MODEL REFINEMENT REFMAC 5.8.0267 MODEL REFINEMENT PHENIX 1.17 MODEL REFINEMENT ERRASER 2 MODEL REFINEMENT ISOLDE 0.9
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 217522