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Human uPAR bound to the Fab fragment of targeted cancer therapeutic antibody FL1
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s)
Type
Source
Accession Code
Details
in silico model
AlphaFold
AF-Q03405-F1-v4
Refinement
RMS Deviations
Key
Refinement Restraint Deviation
f_dihedral_angle_d
9.121
f_angle_d
0.754
f_chiral_restr
0.044
f_plane_restr
0.008
f_bond_d
0.004
Sample
Binary complex of human uPAR and Fab fragment of anti-uPAR antibody FL1
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
FEI VITROBOT MARK IV
Cryogen Name
ETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
184642
Reported Resolution (Å)
2.94
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
FLEXIBLE FIT
Refinement Target
cross-correlation coefficient
Overall B Value
112
Fitting Procedure
Details
An initial local fitting was performed with ISOLDE implemented in ChimeraX prior to real-space refinement in phenix.
Data Acquisition
Detector Type
GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)
10.7
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
TFS KRIOS
Minimum Defocus (nm)
500
Maximum Defocus (nm)
2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
2.7
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
105000
Calibrated Magnification
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
300
Imaging Details
EM Software
Task
Software Package
Version
PARTICLE SELECTION
cryoSPARC
4.5.3
IMAGE ACQUISITION
EPU
3.9
CTF CORRECTION
cryoSPARC
4.5.3
MODEL FITTING
ISOLDE
1.10.1
INITIAL EULER ASSIGNMENT
cryoSPARC
4.5.3
FINAL EULER ASSIGNMENT
cryoSPARC
4.5.3
CLASSIFICATION
cryoSPARC
4.5.3
RECONSTRUCTION
cryoSPARC
4.5.3
MODEL REFINEMENT
PHENIX
1.21.2_5419:
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
CTF corrections were performed after 3D reconstruction to improve the final resolution
7426690
The 7426690 particles were picked by automated particle picking using blob picker. Several rounds of 2D classification were performed to discard particles of low quality, producing 184642 particles of good quality which were used for 3D reconstruction.