7JO8

Crystal structure of a Chimeric Antigen Receptor (CAR) scFv domain rearrangement forming a VL-VL dimer

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6EJG	6ejg, 4yjz, 3auv, 1ktr, 6i07, 1h8n, 5ogi, 6j71
experimental model	PDB	4YJZ	6ejg, 4yjz, 3auv, 1ktr, 6i07, 1h8n, 5ogi, 6j71
experimental model	PDB	3AUV	6ejg, 4yjz, 3auv, 1ktr, 6i07, 1h8n, 5ogi, 6j71
experimental model	PDB	1KTR	6ejg, 4yjz, 3auv, 1ktr, 6i07, 1h8n, 5ogi, 6j71
experimental model	PDB	6I07	6ejg, 4yjz, 3auv, 1ktr, 6i07, 1h8n, 5ogi, 6j71
experimental model	PDB	1H8N	6ejg, 4yjz, 3auv, 1ktr, 6i07, 1h8n, 5ogi, 6j71
experimental model	PDB	5OGI	6ejg, 4yjz, 3auv, 1ktr, 6i07, 1h8n, 5ogi, 6j71
experimental model	PDB	6J71	6ejg, 4yjz, 3auv, 1ktr, 6i07, 1h8n, 5ogi, 6j71

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	295	ammonium sulfate, PEG 400, magnesium sulfate, Tris pH 85.

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.322	α = 90
b = 79.221	β = 109.56
c = 40.616	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	PIXEL	ADSC HF-4M		2019-05-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 19-ID	0.979	NSLS-II	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.399	200	99.8	0.071	0.074	0.022	7.5	11.2		46445

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.42	97.5		1.361	1.44	0.46	0.549		9.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6ejg, 4yjz, 3auv, 1ktr, 6i07, 1h8n, 5ogi, 6j71	1.399	39.61	1.36	46442	2259	99.67	0.1557	0.1549	0.1713	25.0445

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1643
Nucleic Acid Atoms
Solvent Atoms	215
Heterogen Atoms	36

Software

Software
Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.