7XOJ

Cryo-EM structure of GroEL bound to unfolded substrate (UGT1A) at 2.8 Ang. resolution (Consensus Refinement)


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d3.552
f_angle_d0.461
f_chiral_restr0.039
f_bond_d0.003
f_plane_restr0.003
Sample
GroEL-UGT1A complex
Sample Components
GroEL
UDP-glucuronosyltransferase 1A (UGT1A)
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details3 ul of 33 mg/ml GroEL-UGT1A was placed on Holey carbon Quanitifoil copper grids (300 mesh size R1.2/1.3) and blotted for 3 seconds (blot force =1)
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles1202095
Reported Resolution (Å)2.8
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement Target
Overall B Value91
Fitting Procedure
Details
Data Acquisition
Detector TypeFEI FALCON III (4k x 4k)
Electron Dose (electrons/Å**2)40
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1200
Maximum Defocus (nm)2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONRELION3.1
IMAGE ACQUISITIONEPU
IMAGE ACQUISITIONRELION3.1
CTF CORRECTIONCTFFIND4.1
MODEL FITTINGUCSF ChimeraX1.2.5
INITIAL EULER ASSIGNMENTRELION3.1
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX1.19.2-4158
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING ONLYUsing RELIONs own implementation of CTFFIND4.1 --Box 512 --ResMin 30 --ResMax 2 --dFMin 5000 --dFMax 50000 --FStep 250 --dAst 1001289236Parameters for auto picking (LoG) single particles from motion-corrected micrographs with estimated CTF parameters resulted in 1,289,236 particles picked (average of 437 particles per micrograph). All particle images were then extracted with a box size of 300 pixels and a spherical mask diameter of 240 A for 2D classification.