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 8V3B | pdb_00008v3b

Computational Designed Nanocage O43_129_+4


ELECTRON MICROSCOPY
Sample
Computational Designed Nanocage O43_129_+4
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles16878
Reported Resolution (Å)6.4
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryO
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolOTHER
Refinement TargetCross-correlation coefficient
Overall B Value804.6
Fitting Procedure
DetailsComputationally designed model was docked into experimentally derived volume map in ChimeraX. It was then relaxed using Namdinator. Then it was trimme ...Computationally designed model was docked into experimentally derived volume map in ChimeraX. It was then relaxed using Namdinator. Then it was trimmed to polyA in PHENIX.
Data Acquisition
Detector TypeGATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)52
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)800
Maximum Defocus (nm)1800
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC4.4.0
IMAGE ACQUISITIONSerialEM
CTF CORRECTIONcryoSPARC4.4.0
MODEL FITTINGUCSF ChimeraX1.6.1
INITIAL EULER ASSIGNMENTcryoSPARC4.4.0
FINAL EULER ASSIGNMENTcryoSPARC4.4.0
CLASSIFICATIONcryoSPARC4.4.0
RECONSTRUCTIONcryoSPARC4.4.0
MODEL REFINEMENTPHENIXdev-4761
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION23522