6RKU

E. coli DNA Gyrase - DNA binding and cleavage domain in State 1


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3NUH 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d12.934
f_angle_d0.535
f_chiral_restr0.039
f_plane_restr0.021
f_bond_d0.003
Sample
DNA binding and cleavage domain of the E. coli DNA Gyrase in State 1
Sample Components
DNA Gyrase
DNA
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification Instrument
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles60548
Reported Resolution (Å)4
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC2
Map-Model Fitting and Refinement
Id1 (3NUH, 3NUH, 3NUH, 3NUH)
Refinement SpaceREAL
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)50
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)300
Maximum Defocus (nm)800
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS0.01
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification130000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
IMAGE ACQUISITIONSerialEM
CTF CORRECTIONRELION2.0.3
MODEL FITTINGUCSF Chimera1.11.2
MODEL REFINEMENTPHENIX1.12
INITIAL EULER ASSIGNMENTcryoSPARCV1
FINAL EULER ASSIGNMENTRELION2.0.3
RECONSTRUCTIONRELION2.0.3
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION1572962