8P27

Cryo-EM structure of the anaerobic ribonucleotide reductase from Prevotella copri in its dimeric, dATP-bound state


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOther 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d12.0024
f_angle_d0.5303
f_chiral_restr0.0446
f_plane_restr0.0039
f_bond_d0.0036
Sample
Anaerobic ribonucleotide reductase from Prevotella copri in its dimeric, dATP-bound state
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Detailsblot force 1, 5s blot time
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles1009021
Reported Resolution (Å)2.73
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement Targetcorrelation coefficient
Overall B Value40
Fitting Procedure
DetailsManual fitting was done using Coot and automatic real space refinement used phenix.refine
Data Acquisition
Detector TypeGATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)46
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)1000
Maximum Defocus (nm)3400
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification105000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC3.2.0
IMAGE ACQUISITIONEPU2.8.1
CTF CORRECTIONcryoSPARC3.2.0
MODEL FITTINGCoot0.9.8.7
INITIAL EULER ASSIGNMENTcryoSPARC3.3.2
FINAL EULER ASSIGNMENTcryoSPARC4.1.2
CLASSIFICATIONcryoSPARC3.3.2
RECONSTRUCTIONcryoSPARC4.1.2
MODEL REFINEMENTPHENIX1.19.2-4158
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTIONPatch CTF correction in cryoSPARC7544324