2AV1 | pdb_00002av1

Crystal structure of HTLV-1 TAX peptide Bound to Human Class I MHC HLA-A2 with the E63Q and K66A mutations in the heavy chain.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DUZ	PDB Entry 1DUZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	277	PEG3350 20%, MES 0.025M, NaSCN 0.1M, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.5	49.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.328	α = 82.1
b = 62.536	β = 76.39
c = 74.747	γ = 78.1

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	CUSTOM-MADE		2004-04-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.97951	APS	19-BM

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	1.95	20	96.4	0.072	10.29	1.9	63772	61476	1	1	17.73

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)
1	1.95	2.02	91.2		0.302	2.22	1.7	5799

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	PDB Entry 1DUZ	1.95	10	1	62423	57226	3050	96.56	0.17724	0.17724	0.17441	0.17	0.23059	0.23	RANDOM	12.902

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]
0.99	-0.06	0.44	-0.79	0.45	-0.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.557
r_scangle_it	4.62
r_scbond_it	3.113
r_angle_refined_deg	2.048
r_mcangle_it	1.766
r_mcbond_it	1.053
r_symmetry_hbond_refined	0.221
r_xyhbond_nbd_refined	0.217
r_symmetry_vdw_refined	0.192
r_nbd_refined	0.165

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.557
r_scangle_it	4.62
r_scbond_it	3.113
r_angle_refined_deg	2.048
r_mcangle_it	1.766
r_mcbond_it	1.053
r_symmetry_hbond_refined	0.221
r_xyhbond_nbd_refined	0.217
r_symmetry_vdw_refined	0.192
r_nbd_refined	0.165
r_chiral_restr	0.142
r_bond_refined_d	0.021
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6314
Nucleic Acid Atoms
Solvent Atoms	751
Heterogen Atoms	141

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
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.