7AMP | pdb_00007amp

Crystal structure of the complex of HuJovi-1 Fab with the human A6 T-cell receptor TRBC1

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4C56	4C56, 5MEN, 3D85, 1A4J
experimental model	PDB	5MEN	4C56, 5MEN, 3D85, 1A4J
experimental model	PDB	3D85	4C56, 5MEN, 3D85, 1A4J
experimental model	PDB	1A4J	4C56, 5MEN, 3D85, 1A4J

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295	11.2 mg/ml complex in PBS buffer. 0.1 M sodium cacodylate pH 6.0, 3% PEG 8000, 5 mM Zn acetate, 4% benzamidine.

Crystal Properties
Matthews coefficient	Solvent content
3.38	63.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.39	α = 90
b = 91.05	β = 93.82
c = 125.26	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		2017-07-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9282	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.64	54.44	99.9	0.118	0.998	9.9	6.1		38805

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.64	2.69	99.8		1.669	0.625	0.93	6.3

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	4C56, 5MEN, 3D85, 1A4J	2.64	54.44	36928	1877	99.87	0.239	0.2365	0.24	0.2891	0.29	RANDOM	82.765

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]
12.37		0.27	-3.8		-8.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.075
r_dihedral_angle_4_deg	16.537
r_dihedral_angle_3_deg	15.679
r_dihedral_angle_1_deg	6.325
r_angle_refined_deg	1.161
r_angle_other_deg	0.871
r_chiral_restr	0.071
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.075
r_dihedral_angle_4_deg	16.537
r_dihedral_angle_3_deg	15.679
r_dihedral_angle_1_deg	6.325
r_angle_refined_deg	1.161
r_angle_other_deg	0.871
r_chiral_restr	0.071
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6828
Nucleic Acid Atoms
Solvent Atoms	20
Heterogen Atoms	10

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
xia2	data scaling
PHASER	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.