Skip to main content

 3ZEE | pdb_00003zee

Electron cyro-microscopy helical reconstruction of Par-3 N terminal domain


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4I6P 
Sample
PAR-3 N-TERMINAL DUF3534 DOMAIN
Specimen Preparation
Sample Aggregation StateFILAMENT
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification DetailsLIQUID ETHANE
3D Reconstruction
Reconstruction MethodHELICAL
Number of Particles84000
Reported Resolution (Å)6.1
Resolution MethodFSC 0.5 CUT-OFF
Other DetailsTHE INITIAL MODEL WAS OBTAINED USING IHRSR. THEN THE FINAL RECONSTRUCTION WERE OBTAINED BY PROJECTION MATCHING IN EMAN. THE RESOLUTION CRITERIA USED W ...THE INITIAL MODEL WAS OBTAINED USING IHRSR. THEN THE FINAL RECONSTRUCTION WERE OBTAINED BY PROJECTION MATCHING IN EMAN. THE RESOLUTION CRITERIA USED WAS GOLDEN CRITERIA FSC 0.5. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2237. (DEPOSITION ID: 11249).
Refinement TypeHALF-MAPS REFINED INDEPENDENTLY
Symmetry TypeHELICAL
Map-Model Fitting and Refinement
Id1 (4I6P)
Refinement SpaceREAL
Refinement ProtocolOTHER
Refinement TargetENERGY FUNCTION IN NAMD2
Overall B Value
Fitting Procedure
DetailsMETHOD--CROSS CORRELATION REFINEMENT PROTOCOL--X-RAY
Data Acquisition
Detector TypeGATAN ULTRASCAN 4000 (4k x 4k)
Electron Dose (electrons/Å**2)20
Imaging Experiment1
Date of Experiment2010-12-01
Temperature (Kelvin)95
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1800
Maximum Defocus (nm)2500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification96000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging DetailsTHE MICROSCOPE MODEL IS FEI TITAN KRIOS. 6460 RAW IMAGES WERE COLLECTED AUTOMATICALLY USING THE PACKAGE LEGINON. GOOD MICROGRAPHS WERE SELECTED ONE BY ONE
EM Software
TaskSoftware PackageVersion
MODEL FITTINGNAMD2
MODEL FITTINGVMD
RECONSTRUCTIONIMAGIC
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
INDIVIDUAL MICROGRAPHS