7BH1

Cryo-EM Structure of KdpFABC in E1 state with K


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5MRW 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.368
f_angle_d1.121
f_chiral_restr0.059
f_bond_d0.014
f_plane_restr0.007
Sample
KdpFABC in E1 apo state
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details3 uL of protein mixture applied to grid. Blot time 4 seconds, blot force 0, no wait before plunging.
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles202071
Reported Resolution (Å)3.38
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (5MRW)
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement TargetCorrelation coefficient
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K2 QUANTUM (4k x 4k)
Electron Dose (electrons/Å**2)50
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1000
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 Magnification81000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
IMAGE ACQUISITIONSerialEM
CTF CORRECTIONcryoSPARC2.9.0
MODEL FITTINGUCSF Chimera1.14
INITIAL EULER ASSIGNMENTcryoSPARC2.9.0
FINAL EULER ASSIGNMENTcryoSPARC2.9.0
CLASSIFICATIONcryoSPARC2.9.0
RECONSTRUCTIONcryoSPARC2.9.0
MODEL REFINEMENTPHENIX1.18
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION376593template based picker