8QVX

Structure of the PBD of human SRP68/72 (cryoSPARC 3DFlex)


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d4.255
f_angle_d0.646
f_chiral_restr0.04
f_bond_d0.004
f_plane_restr0.004
Sample
SRP68/72
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles145826
Reported Resolution (Å)2.7
Resolution MethodFSC 0.143 CUT-OFF
Other Details3D flexible refinement in cryoSPARC
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeTFS FALCON 4i (4k x 4k)
Electron Dose (electrons/Å**2)70
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)500
Maximum Defocus (nm)2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
Calibrated Magnification245614
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC
PARTICLE SELECTIONTopaz
IMAGE ACQUISITIONEPU
CTF CORRECTIONcryoSPARC
MODEL FITTINGUCSF Chimera
MODEL REFINEMENTPHENIX1.21
INITIAL EULER ASSIGNMENTRELION3
FINAL EULER ASSIGNMENTcryoSPARC
CLASSIFICATIONRELION4
RECONSTRUCTIONcryoSPARC
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION