3DXA | pdb_00003dxa

Crystal Structure of the DM1 TCR in complex with HLA-B*4405 and decamer EBV antigen

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	293	Bicine, Lithium Sulfate, PEG 3350, pH 9.0, vapor diffusion, hanging drop, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.954	α = 90
b = 121.954	β = 90
c = 695.914	γ = 120

Symmetry
Space Group	P 65 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	CCD	MAR CCD 165 mm		2007-03-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1.	APS	17-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3.5	100					40244

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	3.5	100	36429	39229	1970	97.41	0.289	0.289	0.286	0.28	0.33	0.32	RANDOM	63.928

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]
0.21	0.1		0.21		-0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.274
r_dihedral_angle_1_deg	20.746
r_dihedral_angle_3_deg	16.244
r_dihedral_angle_4_deg	15.034
r_angle_refined_deg	1.348
r_angle_other_deg	0.98
r_symmetry_vdw_other	0.251
r_symmetry_vdw_refined	0.249
r_symmetry_hbond_refined	0.236
r_scangle_it	0.236
r_nbd_refined	0.195
r_nbd_other	0.185
r_nbtor_refined	0.18
r_scbond_it	0.162
r_xyhbond_nbd_refined	0.155
r_mcangle_it	0.113
r_chiral_restr	0.108
r_nbtor_other	0.083
r_mcbond_it	0.078
r_mcbond_other	0.028
r_xyhbond_nbd_other	0.011
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.004
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	20168
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction