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Cryo-EM structure of double occupied ring (DOR) of GroEL-UGT1A complex at 2.7 Ang. resolution
ELECTRON MICROSCOPY
Refinement
RMS Deviations
Key
Refinement Restraint Deviation
f_dihedral_angle_d
3.633
f_angle_d
0.478
f_chiral_restr
0.039
f_bond_d
0.003
f_plane_restr
0.003
Sample
Double occupied ring (DOR) of GroEL-UGT1A complex
Sample Components
GroEL
UDP-glucuronosyltransferase 1A (UGT1A)
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
FEI VITROBOT MARK IV
Cryogen Name
ETHANE
Sample Vitrification Details
3 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 Method
SINGLE PARTICLE
Number of Particles
1018943
Reported Resolution (Å)
2.7
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type
POINT
Point Symmetry
C1
Map-Model Fitting and Refinement
Id
1
Refinement Space
REAL
Refinement Protocol
RIGID BODY FIT
Refinement Target
Overall B Value
76.71
Fitting Procedure
Details
Data Acquisition
Detector Type
FEI FALCON III (4k x 4k)
Electron Dose (electrons/Å**2)
40
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
FEI TITAN KRIOS
Minimum Defocus (nm)
1200
Maximum Defocus (nm)
2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
Calibrated Magnification
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
300
Imaging Details
EM Software
Task
Software Package
Version
PARTICLE SELECTION
RELION
3.1
IMAGE ACQUISITION
EPU
IMAGE ACQUISITION
RELION
3.1
CTF CORRECTION
CTFFIND
4.1
MODEL FITTING
UCSF ChimeraX
1.2.5
INITIAL EULER ASSIGNMENT
RELION
3.1
RECONSTRUCTION
RELION
3.1
MODEL REFINEMENT
PHENIX
1.19.2-4158
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING ONLY
Using RELIONs own implementation of CTFFIND4.1 ?
--Box 512
--ResMin 30
--ResMax 2
--dFMin 5000
--dFMax 50000
--FStep 250
--dAst 100
1289236
Parameters for auto picking (LoG) single particles from motion-corrected micrographs with estimated CTF parameters resulted in 1,289,236 particles picked (an 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.