7QPJ | pdb_00007qpj

Crystal structure of engineered TCR (756) complexed to HLA-A*02:01 presenting MAGE-A10 9-mer peptide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7PBC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	293.15	0.2M Sodium chloride, 0.1M MES pH 6.0, 20% w/v PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.197	α = 90
b = 77.446	β = 102.7
c = 116.682	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 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	1.54	77.45	96.9	0.075	0.105	0.073	0.995	6.4	3.2		134415			18.43

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	1.54	1.57	95.8		0.984	1.381	0.967	0.331	1	3.1

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	7PBC	1.54	64.113	134385	6619	96.664	0.204	0.2019	0.21	0.2364	0.25	25.417

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]
-0.768		0.149	-0.793		1.356

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.142
r_dihedral_angle_4_deg	14.894
r_dihedral_angle_3_deg	13.894
r_dihedral_angle_1_deg	7.53
r_lrange_it	6.306
r_lrange_other	6.305
r_scangle_it	4.561
r_scangle_other	4.56
r_mcangle_it	3.556
r_mcangle_other	3.555
r_scbond_it	2.983
r_scbond_other	2.983
r_mcbond_it	2.341
r_mcbond_other	2.34
r_angle_refined_deg	1.631
r_angle_other_deg	1.38
r_xyhbond_nbd_refined	0.211
r_symmetry_nbd_refined	0.2
r_nbd_refined	0.198
r_symmetry_nbd_other	0.193
r_nbd_other	0.188
r_symmetry_xyhbond_nbd_other	0.179
r_symmetry_xyhbond_nbd_refined	0.174
r_nbtor_refined	0.168
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.078
r_bond_refined_d	0.01
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6470
Nucleic Acid Atoms
Solvent Atoms	528
Heterogen Atoms	24

Software

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