7NDQ | pdb_00007ndq

Gag:02 TCR in complex with HLA-E.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5W1W	5W1W, 5EU6
experimental model	PDB	5EU6	5W1W, 5EU6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	23.2% (w/v) PEG 1500, 93 mM MMT pH 9.0

Crystal Properties
Matthews coefficient	Solvent content
3.07	59.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.391	α = 90
b = 89.391	β = 90
c = 293.298	γ = 90

Symmetry
Space Group	P 43 21 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	PIXEL	DECTRIS EIGER2 XE 16M		2020-12-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.55	85.354	100	0.207	0.041	1	11.6	26.3		39941

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.55	2.59			6.926	1.343	0.735	0.3

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	FREE R-VALUE	5W1W, 5EU6	2.551	76.445	39837	1945	99.97	0.242	0.2397	0.25	0.2963	0.3	90.49

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]
0.47			0.47		-0.941

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.261
r_dihedral_angle_3_deg	21.008
r_dihedral_angle_4_deg	19.78
r_dihedral_angle_1_deg	8.835
r_lrange_it	5.058
r_lrange_other	5.057
r_mcangle_it	3.23
r_mcangle_other	3.23
r_scangle_it	2.862
r_scangle_other	2.862
r_mcbond_it	1.932
r_mcbond_other	1.931
r_scbond_it	1.671
r_scbond_other	1.671
r_angle_refined_deg	1.542
r_angle_other_deg	1.136
r_nbd_other	0.253
r_symmetry_xyhbond_nbd_refined	0.239
r_symmetry_xyhbond_nbd_other	0.235
r_nbd_refined	0.208
r_symmetry_nbd_refined	0.207
r_symmetry_nbd_other	0.187
r_xyhbond_nbd_refined	0.179
r_nbtor_refined	0.171
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.057
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_gen_planes_other	0.004
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6544
Nucleic Acid Atoms
Solvent Atoms	13
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
DIALS	data scaling
PHASER	phasing