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CA-SP1 immature lattice assembled in vitro with inhibitor lenacapavir (dialyzed to 50nM)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9D6C
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 9.316 f_angle_d 0.667 f_chiral_restr 0.039 f_plane_restr 0.005 f_bond_d 0.003
Sample Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)
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 835109 Reported Resolution (Å) 2.93 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C6
Map-Model Fitting and Refinement Id 1 (9D6C) Refinement Space Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 50
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS GLACIOS Minimum Defocus (nm) 1400 Maximum Defocus (nm) 2400 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 200 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC IMAGE ACQUISITION SerialEM 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 3929347