Experiment: 6VJA

Structure of CD20 in complex with rituximab Fab

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2OSL

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	16.01
f_angle_d	1.215
f_chiral_restr	0.064
f_bond_d	0.013
f_plane_restr	0.006

Sample
CD20 in complex with rituximab Fab

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	5s blot time

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	149322
Reported Resolution (Å)	3.3
Resolution Method	FSC 0.143 CUT-OFF
Other Details	No data beyond 1/5 A-1 were used in refinement
Refinement Type
Symmetry Type	POINT
Point Symmetry	C2

Map-Model Fitting and Refinement
Id	1 (2OSL)	2
Refinement Space	REAL	REAL
Refinement Protocol	AB INITIO MODEL	FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	Atomic model for CD20 was built ab initio and manually in COOT. It was then re-built using ISOLDE, and finally refined in Phenix.	The X-ray crystallographic atomic model for Rituximab Fab was rigid-body fit into the map, modified using Cootand ISOLDE, and refined with Phenix

Data Acquisition
Detector Type	GATAN K2 QUANTUM (4k x 4k)
Electron Dose (electrons/Å**2)	53

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)
Maximum Defocus (nm)
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	165000
Calibrated Magnification	58906
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cisTEM
IMAGE ACQUISITION	SerialEM
CTF CORRECTION	cisTEM
MODEL FITTING	Coot
INITIAL EULER ASSIGNMENT	cisTEM
FINAL EULER ASSIGNMENT	cisTEM
CLASSIFICATION	cisTEM
RECONSTRUCTION	cisTEM
MODEL REFINEMENT	PHENIX
MODEL FITTING	UCSF Chimera
MODEL FITTING	Coot
MODEL REFINEMENT	PHENIX
MODEL FITTING	ISOLDE

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		4114800	15,630 movies were selected because of the quality of their CTF fits. 4,114,800 coordinates were selected, leading to 466,632 particles which clustered into high-quality 2D class averages