2AQ3 | pdb_00002aq3

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

X-RAY DIFFRACTION

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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	55.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.16	α = 74.18
b = 70.46	β = 75.76
c = 98.37	γ = 88.4

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	100	CCD	ADSC QUANTUM 4		2004-10-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	1.072	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	2.3	40	73.66	0.068		2.4		63758	2	4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.3	2.36	73.66

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	2.3	40	63758	3394	94.21	0.212	0.209	0.206	0.2121	0.271	0.3195	RANDOM	45.433

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]
1.66	-1.17	0.63	0.57	0.54	-2.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.169
r_dihedral_angle_3_deg	24.317
r_dihedral_angle_4_deg	23.204
r_dihedral_angle_1_deg	11.78
r_scangle_it	6.224
r_scbond_it	4.481
r_angle_refined_deg	3.531
r_mcangle_it	2.865
r_mcbond_it	1.795
r_symmetry_vdw_refined	0.365
r_nbtor_refined	0.343
r_symmetry_hbond_refined	0.33
r_nbd_refined	0.32
r_xyhbond_nbd_refined	0.251
r_chiral_restr	0.224
r_bond_refined_d	0.042
r_gen_planes_refined	0.015

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10965
Nucleic Acid Atoms
Solvent Atoms	198
Heterogen Atoms

Software

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