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Gag CA-SP1 immature lattice from intact enveloped virus-like particles
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7ASL
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.7593 f_angle_d 0.5359 f_chiral_restr 0.0377 f_plane_restr 0.0046 f_bond_d 0.0027
Sample Human immunodeficiency virus type 1 group M subtype B (isolate NY5) (HIV-1)
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK III Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 1454696 Reported Resolution (Å) 2.42 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C6
Map-Model Fitting and Refinement Id 1 (7ASL) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 50
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1200 Maximum Defocus (nm) 2200 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 CTF CORRECTION cryoSPARC CTF CORRECTION cryoSPARC CTF CORRECTION cryoSPARC MODEL FITTING UCSF ChimeraX INITIAL EULER ASSIGNMENT cryoSPARC FINAL EULER ASSIGNMENT cryoSPARC CLASSIFICATION cryoSPARC CLASSIFICATION cryoSPARC RECONSTRUCTION cryoSPARC MODEL REFINEMENT PHENIX 1.21_5207 MODEL REFINEMENT Coot 0.98
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION Patch CTF estimation on micrographs; global and local CTF refinement on particles. Both performed in cryoSPARC.