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Structural basis of the activation of the CC chemokine receptor 5 by a chemokine agonist
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5UIW experimental model PDB 5KDO experimental model PDB 6QNK
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.85 f_angle_d 0.521 f_chiral_restr 0.039 f_bond_d 0.003 f_plane_restr 0.003
Sample [6P4]CCL5-CCR5-Gi-Fab16 Sample Components Guanine nucleotide-binding protein G(i) subunit alpha-1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 C-C chemokine receptor type 5 Guanine nucleotide-binding protein G(T) subunit gamma-T1 C-C motif chemokine 5(0-68) Fab
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 345458 Reported Resolution (Å) 3.15 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (5UIW, 5KDO, 5KDO, 5KDO) 2 (5UIW, 6QNK, 6QNK) Refinement Space REAL REAL Refinement Protocol FLEXIBLE FIT 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) 49
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS GLACIOS Minimum Defocus (nm) Maximum Defocus (nm) 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 MODEL FITTING Coot 0.9 RECONSTRUCTION cryoSPARC 3.10 MODEL REFINEMENT PHENIX 1.19 MODEL FITTING UCSF Chimera MODEL REFINEMENT PHENIX 1.19
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details NONE