7OZ3

S. agalactiae BusR in complex with its busA-promotor DNA


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7B5T 
experimental modelPDB 7B5U 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d23.1439
f_angle_d1.3535
f_chiral_restr0.0768
f_bond_d0.0086
f_plane_restr0.005
Sample
transcriptional repressor BusR bound to target DNA
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification Instrument
Cryogen NameETHANE
Sample Vitrification Details0.05% beta-octyl glycoside added prior to plunge freezing
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles112451
Reported Resolution (Å)4.46
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (7B5T, 7B5U)
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement Target
Overall B Value177
Fitting Procedure
DetailsRCK_C domains were build by rigid body fit of the model 7B5U. The flexible linker between RCK_C domain and coiled-coil domain were build de novo.
Data Acquisition
Detector TypeGATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)45
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
IMAGE ACQUISITIONEPU
CTF CORRECTIONRELION3.1.2
MODEL FITTINGCoot0.9.5
INITIAL EULER ASSIGNMENTRELION
FINAL EULER ASSIGNMENTRELION
CLASSIFICATIONRELION3.1.2
RECONSTRUCTIONRELION3.1.2
MODEL REFINEMENTPHENIX1.19
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION