ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d9.169
f_angle_d1.252
f_chiral_restr0.064
f_bond_d0.018
f_plane_restr0.007
Sample
AcrABTolC in apo state
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Detailsa 3ul aliquot at a concentration of 2 mg per ml was applied onto glow-discharged holey carbon grid (Quantifoil Au R1.21.3, 300 mesh)
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles13544
Reported Resolution (Å)6.5
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC3
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement TargetCross-correlation coefficient
Overall B Value
Fitting Procedure
DetailsCrystal structures were rigid-body fit into the density map and model optimization was then carried out with Phenix real-space refine. Due to the weak ...Crystal structures were rigid-body fit into the density map and model optimization was then carried out with Phenix real-space refine. Due to the weaker resolution, stronger stereochemical and secondary structure restraints were used to ensure that alpha-helices and beta-sheets did not deviate far from their expected geometry. Manual adjustments were kept to a minimum to reduce human bias in the modeling procedure, with Coot only being used to fix obvious errors such as C-beta deviations. A final check of MolProbity and cross correlation was done to ensure model quality.
Data Acquisition
Detector TypeGATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)1
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)
Maximum Defocus (nm)
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
PARTICLE SELECTIONRELION2
CTF CORRECTIONCTFFIND4
MODEL FITTINGUCSF Chimera
INITIAL EULER ASSIGNMENTEMAN2.2
FINAL EULER ASSIGNMENTRELION2
MODEL REFINEMENTPHENIX
MODEL REFINEMENTCoot
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING ONLY95410auto box by relion