8PVV

Archaeoglobus fulgidus AfAgo complex with AfAgo-N protein (fAfAgo) bound with 30 nt RNA guide and 51 nt DNA target


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8OK9 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d19.032
f_angle_d0.565
f_chiral_restr0.043
f_plane_restr0.005
f_bond_d0.003
Sample
AfAgo and AfAgo-N complex with 30 nt RNA guide and 51 nt DNA target
Sample Components
Piwi protein
Archaeoglobus fulgidus AfAgo-N protein
RNA (30-MER)
DNA (51-MER)
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles498038
Reported Resolution (Å)2.81
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (8ok9, 8ok9)
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeFEI FALCON III (4k x 4k)
Electron Dose (electrons/Å**2)31
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS GLACIOS
Minimum Defocus (nm)1000
Maximum Defocus (nm)2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelOTHER
Nominal Magnification92000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)200
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARCv.4.2.1
MODEL REFINEMENTPHENIX1.18.2_3874:
IMAGE ACQUISITIONEPU
MASKINGUCSF Chimera1.17.1
CTF CORRECTIONcryoSPARCv.4.2.1
MODEL FITTINGUCSF Chimera1.17.1
OTHERCoot0.9
INITIAL EULER ASSIGNMENTcryoSPARCv.4.2.1
FINAL EULER ASSIGNMENTcryoSPARCv.4.2.1
CLASSIFICATIONcryoSPARCv.4.2.1
RECONSTRUCTIONcryoSPARCv.4.2.1
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
NONE2326555Blob particle picking