7B5O

Cryo-EM structure of the human CAK bound to ICEC0942 at 2.5 Angstroms resolution


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6XBZ 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d17.666
f_angle_d0.717
f_chiral_restr0.05
f_bond_d0.007
f_plane_restr0.006
Sample
CDK-activating kinase (CAK) in complex with 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; ligand coordinates from PHENIX-OPLS3e refinement
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 CORRECTIONImplemented in RELION 3.110904715