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Local refinement of Plasmodium falciparum gametocyte surface protein Pfs48/45 Domains 1 and 2 in complex with neutralizing antibodies
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7ZXG
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.944 f_angle_d 0.892 f_chiral_restr 0.088 f_plane_restr 0.007 f_bond_d 0.004
Sample complex of Pfs48/45, RUPA58 and RUPA154
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument LEICA EM GP Cryogen Name ETHANE Sample Vitrification Details sample was frozen with Leica Automatic Plunge Freezer EM GP2
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 306744 Reported Resolution (Å) 3.3 Resolution Method FSC 0.143 CUT-OFF Other Details Local refinement was performed with a mask including domains D1 and D2 of Pfs48/45 and variable regions of RUPA-58 and RUPA-154 Fabs Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (7ZXG, 8U70, 8U70) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON IV (4k x 4k) Electron Dose (electrons/Å**2) 48.69
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 500 Maximum Defocus (nm) 2000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification 75000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4 IMAGE ACQUISITION EPU 2 CTF CORRECTION cryoSPARC 4 MODEL FITTING UCSF Chimera CLASSIFICATION cryoSPARC 4 RECONSTRUCTION cryoSPARC 4 MODEL REFINEMENT PHENIX 1.19
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 6424191