9GCM | pdb_00009gcm

Structure of the U11 snRNP core


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFoldAF-Q9BV90-F1 
in silico modelAlphaFoldAF-Q16560-F1 
in silico modelAlphaFoldAF-Q8N8D1-F1 
Sample
Structure of the U11 snRNP core
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles268233
Reported Resolution (Å)3.1
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement TargetCross-correction coefficient
Overall B Value71.2
Fitting Procedure
Detailsrefinement is done in Phenix
Data Acquisition
Detector TypeFEI FALCON IV (4k x 4k)
Electron Dose (electrons/Å**2)41.73
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)700
Maximum Defocus (nm)1700
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification165000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging DetailsPreliminary grid screening was performed on Glacios.
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARCv4.3.1
IMAGE ACQUISITIONSerialEM
MODEL FITTINGUCSF ChimeraX1.6.1
INITIAL EULER ASSIGNMENTcryoSPARCv4.3.1
FINAL EULER ASSIGNMENTcryoSPARCv4.3.1
CLASSIFICATIONcryoSPARCv4.3.1
RECONSTRUCTIONcryoSPARCv4.3.1
MODEL REFINEMENTPHENIX1.20.1
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
NONE7144222Topaz picking is performed with user-trained model