2AQ1 | pdb_00002aq1

Crystal structure of T-cell receptor V beta domain variant complexed with superantigen SEC3 mutant

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	20% PEG 3350, 0.2M tri-ammonium citrate, 0.3% dioxane, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.8	55.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.2	α = 74.79
b = 70.186	β = 75.05
c = 98.403	γ = 88.54

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray						M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	1.0722	NSLS	X25

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.1	40	89.8	0.034		2.5		81743	2	4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.1	2.18	79.9	66	0.222		2.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	2.1	35	91912	81743	4468	95.98	0.188	0.187	0.185	0.1952	0.243	0.1967	RANDOM	45.303

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]
2.36	-0.62	0.88	-0.95	0.35	-2.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.949
r_dihedral_angle_3_deg	17.68
r_dihedral_angle_4_deg	14.4
r_dihedral_angle_1_deg	7.841
r_scangle_it	4.45
r_scbond_it	3.127
r_mcangle_it	2.322
r_angle_refined_deg	2.016
r_mcbond_it	1.401
r_nbtor_refined	0.311

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.949
r_dihedral_angle_3_deg	17.68
r_dihedral_angle_4_deg	14.4
r_dihedral_angle_1_deg	7.841
r_scangle_it	4.45
r_scbond_it	3.127
r_mcangle_it	2.322
r_angle_refined_deg	2.016
r_mcbond_it	1.401
r_nbtor_refined	0.311
r_nbd_refined	0.244
r_symmetry_hbond_refined	0.212
r_xyhbond_nbd_refined	0.182
r_symmetry_vdw_refined	0.178
r_chiral_restr	0.145
r_bond_refined_d	0.024
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11089
Nucleic Acid Atoms
Solvent Atoms	584
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOLREP	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.