7PDW

Crystal structure of parent TCR (728) complexed to HLA-A*02:01 presenting MAGE-A10 9-mer peptide

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	0.02M Sodium/potassium phosphate, 0.1M Bis-Tris propane pH 6.5, 20% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.6572	53.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.081	α = 109.17
b = 95.834	β = 96.51
c = 106.261	γ = 99.7

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	PIXEL	DECTRIS PILATUS3 6M		2018-05-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97625	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.82	98.71	90.2	0.098	0.139	0.098	0.986	4.7	1.5		158062

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.82	1.85			0.672	0.95	0.672	0.464	0.7	1.4

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7PBC	1.82	81.936	158060	8035	90.166	0.203	0.2028	0.2013	0.2292	Random selection	36.993

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]
-2.023	0.947	0.098	2.143	0.857	-0.991

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.684
r_dihedral_angle_4_deg	14.923
r_dihedral_angle_3_deg	14.33
r_dihedral_angle_1_deg	7.622
r_lrange_it	7.273
r_lrange_other	7.265
r_scangle_it	5.245
r_scangle_other	5.238
r_mcangle_other	4.376
r_mcangle_it	4.375
r_scbond_it	3.39
r_scbond_other	3.378
r_mcbond_it	2.912
r_mcbond_other	2.91
r_angle_refined_deg	1.471
r_angle_other_deg	1.277
r_nbd_refined	0.197
r_symmetry_nbd_other	0.184
r_nbd_other	0.184
r_xyhbond_nbd_refined	0.166
r_nbtor_refined	0.164
r_symmetry_nbd_refined	0.142
r_symmetry_xyhbond_nbd_refined	0.135
r_ncsr_local_group_4	0.091
r_ncsr_local_group_1	0.079
r_ncsr_local_group_2	0.078
r_symmetry_nbtor_other	0.077
r_symmetry_xyhbond_nbd_other	0.072
r_chiral_restr	0.067
r_ncsr_local_group_3	0.065
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13024
Nucleic Acid Atoms
Solvent Atoms	644
Heterogen Atoms	17

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
Coot	model building