5TQW

CryoEM reconstruction of human IKK1, open conformation 1


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d4.821
f_angle_d1.008
f_chiral_restr0.054
f_bond_d0.007
f_plane_restr0.007
Sample
Inhibitor of KappaB Kinase 1 dimer
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentHOMEMADE PLUNGER
Cryogen NameETHANE
Sample Vitrification DetailsSample containing IKK1 dimers in SEC buffer was applied onto freshly plasma-treated (6 seconds, Gatan Solarus plasma cleaner) holey carbon C-flat grid ...Sample containing IKK1 dimers in SEC buffer was applied onto freshly plasma-treated (6 seconds, Gatan Solarus plasma cleaner) holey carbon C-flat grids (Protochips), adsorbed for 30 seconds, and then plunged into liquid ethane using a manual cryo-plunger in an ambient environment of 4 degrees C.
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles24987
Reported Resolution (Å)5.6
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC2
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement TargetFSC 0.5
Overall B Value340
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)40
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification22500
Calibrated Magnification38167
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONFindEM
IMAGE ACQUISITIONLeginon3.1
CTF CORRECTIONCTFFIND
INITIAL EULER ASSIGNMENTRELION1.3
FINAL EULER ASSIGNMENTFREALIGN9.11
CLASSIFICATIONFREALIGN9.11
RECONSTRUCTIONFREALIGN9.11
MODEL REFINEMENTRosetta2015.12.57698
MODEL REFINEMENTPHENIXdev-2499
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTIONwithin Relion and Frealign230242