9QWK | pdb_00009qwk

Crystal structure of S2c-a5b6 TCR in complex with CD1c

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3OV6
experimental model	PDB	4P4K
experimental model	PDB	5FK9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2 M Sodium thiocyanate and 20 % (w/v) PEG 3350

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.233	α = 91.85
b = 83.652	β = 95.99
c = 180.13	γ = 115.61

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 EIGER2 XE 16M		2024-04-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9537	Diamond	I04

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	2.27	89.24	98.52	0.101	0.119	0.063	0.963	14.6	3.6		194208

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	2.27	2.31	96.77		1.66	1.943	1.004	0.325	0.8	3.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.27	89.24	192181	2022	98.52	0.22653	0.22626	0.239	0.25287	0.2672	RANDOM	72.912

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]
3.15	1.25	-0.46	-1.64	1.85	-2.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.935
r_dihedral_angle_2_deg	11.622
r_long_range_B_refined	7.94
r_long_range_B_other	7.94
r_dihedral_angle_1_deg	7.599
r_scangle_other	5.646
r_mcangle_it	4.811
r_mcangle_other	4.81
r_scbond_it	3.659
r_scbond_other	3.659
r_mcbond_it	3.088
r_mcbond_other	3.088
r_angle_refined_deg	1.63
r_angle_other_deg	0.585
r_chiral_restr	0.117
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
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	25763
Nucleic Acid Atoms
Solvent Atoms	82
Heterogen Atoms	332

Software

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