7AMR | pdb_00007amr

Crystal structure of the complex of the KFN mutant of Jovi-1 Fab with human TRBC1

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295	Equimolar amounts of A6 TCR C1 and Fab were mixed in PBS) to 10.8 mg/ml. 9% PEG 8000, 0.1M sodium cacodylate pH 6.6, 5 mM ZnCl2, 2% benzamidine HCl. Crystals from the complex with huJovi-1 Fab were used as seeds.

Crystal Properties
Matthews coefficient	Solvent content
3.28	62.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 115.694	α = 90
b = 91.011	β = 93.89
c = 123.311	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	100	PIXEL	DECTRIS PILATUS 6M-F		2018-08-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9762	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	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	1.95	45.7	53.7	0.125	0.056	0.996	10.4	5.7		49996

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2.13	11.6		1.018	0.509	0.524	1.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6***	1.949	43.59	49988	2398	53.7	0.1817	0.1794	0.18	0.2252	0.23	RANDOM	31.74

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]
5.7244		-0.2398	-2.0646		-3.6599

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	18.46
t_omega_torsion	3.64
t_angle_deg	1.05
t_bond_d	0.008
t_dihedral_angle_d
t_gen_planes
t_it
t_chiral_improper_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6833
Nucleic Acid Atoms
Solvent Atoms	683
Heterogen Atoms	23

Software

Software
Software Name	Purpose
BUSTER	refinement
XDS	data reduction
STARANISO	data scaling
REFMAC	phasing

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 R01GM157729.