8E27

RNA-free Human Dis3L2


ELECTRON MICROSCOPY
Sample
Inactive RNA-free HsDis3L2 (D391N)
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles162793
Reported Resolution (Å)3.4
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (4PMW)
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
DetailsChain A of PDB 4PMW (MmDis3L2) was fit into the map via rigid body fitting. Residues were then mutated to match the human protein and manual building ...Chain A of PDB 4PMW (MmDis3L2) was fit into the map via rigid body fitting. Residues were then mutated to match the human protein and manual building done to correct for differences. Next rounds of refinement and building were done in PHENIX and Coot, respectively, until the final structure was obtained.
Data Acquisition
Detector TypeGATAN K2 QUANTUM (4k x 4k)
Electron Dose (electrons/Å**2)51.75
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)700
Maximum Defocus (nm)2600
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification160000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONWarp1.0.8
IMAGE ACQUISITIONEPU2.5
CTF CORRECTIONWarp1.0.8
MODEL FITTINGCoot
INITIAL EULER ASSIGNMENTcryoSPARC3.0.0
FINAL EULER ASSIGNMENTcryoSPARC3.0.0
CLASSIFICATIONcryoSPARCv3.0.0
RECONSTRUCTIONcryoSPARC3.0.0
MODEL REFINEMENTPHENIX1.18-3855-000
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING ONLY990287