2IAM

Structural basis for recognition of mutant self by a tumor-specific, MHC class II-restricted TCR

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1FYT	1FYT, 1IAL
experimental model	PDB	1IAL	1FYT, 1IAL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	295	8% PEG6000, 0.1M di-ammonium phosphate, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.02	59.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.391	α = 90
b = 270.542	β = 90
c = 97.396	γ = 90

Symmetry
Space Group	C 2 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV		2005-08-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.54

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	2.8	50	92.8	0.091	10.7			26581

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)
	2.8	2.94	91.9		0.513	3		5639

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1FYT, 1IAL	2.8	41.91	26375	25046	1329	92.16	0.21051	0.20693	0.27915	RANDOM	62.8

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]
-5.39			4.95		0.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.547
r_dihedral_angle_3_deg	21.109
r_dihedral_angle_4_deg	18.69
r_dihedral_angle_1_deg	10.92
r_scangle_it	2.944
r_angle_refined_deg	1.96
r_scbond_it	1.908
r_mcangle_it	1.278
r_mcbond_it	0.752
r_nbtor_refined	0.322
r_symmetry_vdw_refined	0.256
r_nbd_refined	0.253
r_xyhbond_nbd_refined	0.178
r_chiral_restr	0.117
r_symmetry_hbond_refined	0.043
r_bond_refined_d	0.019
r_gen_planes_refined	0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6511
Nucleic Acid Atoms
Solvent Atoms	40
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
PHASER	phasing