8EAM

SsoMCM hexamer bound to Mg/ADP-BeFx and DNA. Class 2. Merged particles from datasets with 3 different DNA entities


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d6.286
f_angle_d0.453
f_chiral_restr0.044
f_plane_restr0.003
f_bond_d0.002
Sample
SsoMCM hexamer bound to Mg/ADP-BeFx and DNA. Class 2. Merged particles from datasets with 3 different DNA entities.
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification Instrument
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles1493596
Reported Resolution (Å)2.59
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (6MII)
Refinement SpaceREAL
Refinement ProtocolOTHER
Refinement Target
Overall B Value
Fitting Procedure
DetailsBond distance and angle restraints for a tetrahedral Zn2+ coordination were applied. Bond distance and angle restraints for a octahedral Mg2+ coordina ...Bond distance and angle restraints for a tetrahedral Zn2+ coordination were applied. Bond distance and angle restraints for a octahedral Mg2+ coordination were applied.
Data Acquisition
Detector TypeGATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)78
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)800
Maximum Defocus (nm)1800
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC
IMAGE ACQUISITIONSerialEM
CTF CORRECTIONcryoSPARC2.14.2
MODEL FITTINGPHENIX1.20.1_4487
INITIAL EULER ASSIGNMENTcryoSPARC2.14.2
FINAL EULER ASSIGNMENTcryoSPARC3.31
CLASSIFICATIONcryoSPARC3.31
RECONSTRUCTIONcryoSPARC3.31
MODEL REFINEMENTPHENIX1.20.1_4487
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTIONInitial CTF was calculated by cryoSPARC Patch CTF. CTF parameters were refined during final homogeneous refinement in cryoSPARC.Particles were merged from 3 different datasets that differ in the specific DNA present. The particles for each individual structure were selected in equivalent ways: Particles were selected from a subset of micrographs with cryoSPARC blob picker. 2D class averages were calculated, selected and used as templates with cryoSPARC template picker.