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 6W18 | pdb_00006w18

Structure of S. pombe Arp2/3 complex in inactive state


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DWL 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d19.484
f_angle_d0.5135
f_chiral_restr0.0408
f_bond_d0.0025
f_plane_restr0.0018
Sample
Arp2/3 complex
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentHOMEMADE PLUNGER
Cryogen NameETHANE
Sample Vitrification Details4 uL of sample was applied to freshly glow-discharged grid. Excess sample was manually blotted off with a dry Whatman No.1 filter paper for 5-7 second ...4 uL of sample was applied to freshly glow-discharged grid. Excess sample was manually blotted off with a dry Whatman No.1 filter paper for 5-7 seconds. Immediately after the blotting step the sample containing grid was rapidly vitrified by plunge freezing into liquid ethane.
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles112170
Reported Resolution (Å)4.2
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (3DWL)
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeFEI FALCON III (4k x 4k)
Electron Dose (electrons/Å**2)44.34
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TALOS ARCTICA
Minimum Defocus (nm)-700
Maximum Defocus (nm)-1300
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification120000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)200
Imaging DetailsData were collected by combining untilted and tilted (20, 30 and 40 degrees) images. Stage shifting to the targeted exposure position was used for navigation during data acquisition.
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC2.12.4
IMAGE ACQUISITIONEPU2.2.0.65
CTF CORRECTIONcryoSPARC2.12.4
MODEL FITTINGNAMD
MODEL FITTINGCoot
MODEL FITTINGUCSF Chimera
FINAL EULER ASSIGNMENTcryoSPARC2.12.4
CLASSIFICATIONcryoSPARC2.12.4
RECONSTRUCTIONcryoSPARC2.12.4
MODEL REFINEMENTPHENIX
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTIONLocal CTF estimation was performed for all micrographs using the CTF estimation package within cryoSPARC.3336981Automated Gaussian-based blob picker was used.