ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d7.4095
f_angle_d0.4396
f_chiral_restr0.0401
f_bond_d0.0025
f_plane_restr0.0025
Sample
SLFN12-PDE3A complex, SLFN12 body
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details4.5 second blot time
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles247402
Reported Resolution (Å)2.76
Resolution MethodFSC 0.143 CUT-OFF
Other DetailsMulti-body refinement in Relion
Refinement Type
Symmetry TypePOINT
Point SymmetryC2
Map-Model Fitting and Refinement
Id1 (5YD0)
Refinement SpaceREAL
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
DetailsThe atomic model (including per-residue ADP/B-factors) was refined in Phenix against the sharpened/local resolution-filtered map
Data Acquisition
Detector TypeGATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)50
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification81000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
IMAGE ACQUISITIONEPU2.5
CTF CORRECTIONCTFFIND4.1.13
INITIAL EULER ASSIGNMENTcisTEM1.0.0-beta
FINAL EULER ASSIGNMENTRELION3.1
CLASSIFICATIONRELION3.1
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX1.18
MODEL REFINEMENTCoot0.8.9
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTIONCTF correction was applied throughout the entire processing workflow, beginning with particle picking2160426