7NDU | pdb_00007ndu

Gag:02 TCR in complex with HLA-E featuring a non-natural amino acid

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	22.3% (w/v) PEG 1500, 89 mM MMT pH 9.0

Crystal Properties
Matthews coefficient	Solvent content
3.13	60.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.98	α = 90
b = 88.98	β = 90
c = 293.57	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		2020-12-03	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	2.9	61.597	99.9	0.23	0.082	0.998	8.6	8.8		27166

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	2.9	2.95	99.2		2.569	0.933	0.458	1	8.3

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	7NDQ	2.9	61.597	27136	1336	99.823	0.245	0.2419	0.24	0.3015	0.3	68.718

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]
1.801			1.801		-3.602

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.574
r_dihedral_angle_4_deg	19.529
r_dihedral_angle_3_deg	19.164
r_dihedral_angle_1_deg	8.752
r_angle_refined_deg	1.588
r_angle_other_deg	1.135
r_symmetry_nbd_refined	0.225
r_nbd_refined	0.215
r_xyhbond_nbd_refined	0.187
r_nbd_other	0.187
r_symmetry_nbd_other	0.183
r_nbtor_refined	0.173
r_symmetry_xyhbond_nbd_refined	0.173
r_symmetry_xyhbond_nbd_other	0.096
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.058
r_bond_refined_d	0.007
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	6529
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

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