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CryoEM structure of the Nipah virus nucleocapsid spiral clam-shaped assembly
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7NT5
Refinement RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 35.24 r_mcangle_it 28.663 r_mcbond_it 19.206 r_scbond_it 14.11 r_dihedral_angle_1_deg 8.138 r_angle_refined_deg 1.96 r_chiral_restr 0.123 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 35.24 r_mcangle_it 28.663 r_mcbond_it 19.206 r_scbond_it 14.11 r_dihedral_angle_1_deg 8.138 r_angle_refined_deg 1.96 r_chiral_restr 0.123 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_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 (48-MER) RNA (42-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 23029 Reported Resolution (Å) 4.3 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (7NT5) 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