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Structure of NaCT-PF4a complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7JSK
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 6.775 f_angle_d 0.639 f_chiral_restr 0.042 f_plane_restr 0.006 f_bond_d 0.004
Sample Dimer of NaCT in complex with PF4a
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 745845 Reported Resolution (Å) 2.13 Resolution Method FSC 0.143 CUT-OFF Other Details Non-uniform refinement and local refinement with a mask Refinement Type Symmetry Type POINT Point Symmetry C2
Map-Model Fitting and Refinement Id 1 (7jsk) Refinement Space REAL Refinement Protocol OTHER Refinement Target cross-correlation coefficient Overall B Value 43.93 Fitting Procedure Details Initial local fitting was done using Chimera and then coot was used for ajustment.
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 61.19
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1200 Maximum Defocus (nm) 1600 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 105000 Calibrated Magnification 105000 Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION Warp 1.0.9 PARTICLE SELECTION Topaz 0.2.5a IMAGE ACQUISITION Leginon 3.5 CTF CORRECTION cryoSPARC 3.3.1 MODEL FITTING UCSF Chimera 1.15 MODEL FITTING Coot 0.9.6 MODEL REFINEMENT PHENIX 1.19.2 INITIAL EULER ASSIGNMENT cryoSPARC 3.3.1 FINAL EULER ASSIGNMENT cryoSPARC 3.3.1 CLASSIFICATION cryoSPARC 3.3.1 RECONSTRUCTION cryoSPARC 3.3.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION CTF amplitude correction was performed after particle polishing 6132038 Particles were selected from 5227 untilted images and 6942 40 degree tilted images