7UL6

CryoEM structure of full-length dimeric ClbP


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7MDF 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d4.777
f_angle_d0.551
f_chiral_restr0.042
f_plane_restr0.006
f_bond_d0.003
Sample
ClbP
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification DetailsThree uL of sample were deposited onto 400 mesh Quantifoil Cu 1.2/1.3 grids that had been glow discharged in a PELCO easiGLOW (Ted Pella) at 0.39 mBar ...Three uL of sample were deposited onto 400 mesh Quantifoil Cu 1.2/1.3 grids that had been glow discharged in a PELCO easiGLOW (Ted Pella) at 0.39 mBar, 15 mA for 30 s. Samples were vitrified in 100% liquid ethane using a Vitrobot Mark IV (Thermo Fisher Scientific), with a wait time of 30 s, blot time of 5 s and a blot force of 16 at 100% humidity.
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles109906
Reported Resolution (Å)3.73
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC2
Map-Model Fitting and Refinement
Id1 (7MDF)
Refinement SpaceREAL
Refinement ProtocolAB INITIO MODEL
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)76.191
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)800
Maximum Defocus (nm)2200
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification105000
Calibrated Magnification60606
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
IMAGE ACQUISITIONSerialEM3.8.6
CTF CORRECTIONRELION3.1.1
MODEL FITTINGCoot0.93
MODEL FITTINGISOLDE1.0b4.dev0
MODEL FITTINGUCSF Chimera1.15
FINAL EULER ASSIGNMENTcryoSPARC
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX1.20.1-4487
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION562462