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 6BBM | pdb_00006bbm

Mechanisms of Opening and Closing of the Bacterial Replicative Helicase: The DnaB Helicase and Lambda P Helicase Loader Complex


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2R5U 
experimental modelPDB 3BH0 
Sample
DnaB helicase - Lambda P helicase loader DNA replication complex
Sample Components
E coli DnaB helicase
Lambda P helicase loader
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details3uL of sample was adhered to a fresh plasma cleaned grid and allowed to adsorb for 30 seconds, blotted for 3 seconds with a blot force of 4 and plunge ...3uL of sample was adhered to a fresh plasma cleaned grid and allowed to adsorb for 30 seconds, blotted for 3 seconds with a blot force of 4 and plunge frozen into liquid nitrogen-cooled ethane.
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles90883
Reported Resolution (Å)4.1
Resolution MethodFSC 0.143 CUT-OFF
Other DetailsRelion was used to independently refine half sets using 0.143 gold-standard to a resolution of 4.1A. A total of 90,883 particles went into this recons ...Relion was used to independently refine half sets using 0.143 gold-standard to a resolution of 4.1A. A total of 90,883 particles went into this reconstruction.
Refinement Type
Symmetry Type
Map-Model Fitting and Refinement
Id1 (2R5U, 3BH0)
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
DetailsThe initial fitting was done with the 2R5U and 3BH0 models onto which the E. coli amino sequence had been built. The linker segments that connected t ...The initial fitting was done with the 2R5U and 3BH0 models onto which the E. coli amino sequence had been built. The linker segments that connected these segments were built by hand. PHENIX real_space_refine was used to refine the complete model for the B6P5 entity.
Data Acquisition
Detector TypeGATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)8
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)-1
Maximum Defocus (nm)-3
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification22500
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging DetailsPreliminary grid screening was performed prior to Krios data collections. All microscope alignments were completed by the New York Structural Biology SEMC team.
EM Software
TaskSoftware PackageVersion
IMAGE ACQUISITIONLeginon0.0
IMAGE ACQUISITIONAppion0.0
IMAGE ACQUISITIONAppion0.0
CTF CORRECTIONGctf
MODEL FITTINGMOLREP
MODEL FITTINGCoot
SERIES ALIGNMENTRELION
SERIES ALIGNMENTGautomatch
SERIES ALIGNMENTEMAN2
RECONSTRUCTIONRELION
SERIES ALIGNMENTTOMO3D
SERIES ALIGNMENTDynamo
SERIES ALIGNMENTEMAN2
RECONSTRUCTIONDynamo
MODEL REFINEMENTPHENIX
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTIONCTF correction was performed before data processing on summed micrographs using Gctf.