7ZBT

Subtomogram averaging of Rubisco from native Halothiobacillus carboxysomes


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1SVD 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d4.345
f_angle_d0.778
f_chiral_restr0.043
f_bond_d0.008
f_plane_restr0.005
Sample
alpha carboxysomes
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification Instrument
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSUBTOMOGRAM AVERAGING
Number of Particles149479
Reported Resolution (Å)3.3
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryD4
Map-Model Fitting and Refinement
Id1 (1SVD)
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement Target
Overall B Value94.7
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K2 QUANTUM (4k x 4k)
Electron Dose (electrons/Å**2)3
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1500
Maximum Defocus (nm)6000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
IMAGE ACQUISITIONSerialEM
CTF CORRECTIONemClarity
MODEL FITTINGCoot
FINAL EULER ASSIGNMENTemClarity
RECONSTRUCTIONemClarity
MODEL REFINEMENTUCSF Chimera
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION