7B5Q

Cryo-EM structure of the human CAK bound to ICEC0942 (PHENIX-OPLS3e)


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6XBZ 
Sample
CDK-activating kinase bound to ICEC0942
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE-PROPANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles205478
Reported Resolution (Å)2.5
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (6XBZ)
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
DetailsReal space refinement in PHENIX combined with the OPLS3e force field (Schrodinger 2020-3).
Data Acquisition
Detector TypeGATAN K3 (6k x 4k)GATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)6969
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TALOS ARCTICA
Minimum Defocus (nm)500
Maximum Defocus (nm)1500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
Calibrated Magnification72886
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)200
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONRELION3.1
IMAGE ACQUISITIONSerialEM
CTF CORRECTIONCTFFIND4.1
CTF CORRECTIONRELION3.1
MODEL FITTINGUCSF Chimera
MODEL FITTINGCoot
INITIAL EULER ASSIGNMENTRELION3.1
FINAL EULER ASSIGNMENTRELION3.1
CLASSIFICATIONRELION3.1
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION10904715