6FR6 | pdb_00006fr6

HA1.7 Human T-Cell Receptor specific for Influenza virus epitope PKYVKQNTLKLAT presented by Human Leukocyte Antigen HLA-DR0101

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6EH8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	291	20% PEG 8K, 0.1 M Tris, 0.2M NH4SO4

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70	α = 90
b = 50.24	β = 93.31
c = 73.17	γ = 90

Symmetry
Space Group	P 1 21 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	PIXEL	DECTRIS PILATUS3 S 6M		2011-01-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.9795	Diamond	I02

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.98	36.52	98.8	0.096	0.132	11.6	4		10488

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.98	3.06	99.5		0.54	0.736	2.3	4.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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	6EH8	2.98	36.52	9958	502	98.79	0.20545	0.20074	0.2	0.29906	0.29	RANDOM	57.738

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]
-1.32		1.11	-1.4		2.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.396
r_dihedral_angle_3_deg	21.569
r_dihedral_angle_4_deg	20.624
r_dihedral_angle_1_deg	9.944
r_long_range_B_refined	2.97
r_long_range_B_other	2.97
r_angle_refined_deg	1.957
r_angle_other_deg	1.11
r_mcangle_it	1.096
r_mcangle_other	1.096
r_scangle_other	0.891
r_mcbond_it	0.616
r_mcbond_other	0.616
r_scbond_it	0.583
r_scbond_other	0.504
r_chiral_restr	0.108
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3508
Nucleic Acid Atoms
Solvent Atoms	19
Heterogen Atoms	10

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
xia2	data reduction
SCALA	data scaling
PHASER	phasing