8D5Q | pdb_00008d5q

TCR TG6 in complex with Ld-HF10

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1LD9	1LD9, 3TO4
experimental model	PDB	3TO4	1LD9, 3TO4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277	11 % w/v PEG 8000, 0.1 M MES 6.0, 0.24 M Ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.92	57.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.963	α = 90
b = 89.963	β = 90
c = 105.982	γ = 90

Symmetry
Space Group	P 41

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 EIGER X 16M		2018-02-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.9792	APS	24-ID-E

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rpim I (All)	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	2.5	90	99.8	0.03	26.6	6.4		29168

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.54			0.29

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	NONE	1LD9, 3TO4	2.501	45.022	29168	1493	99.839	0.172	0.1688	0.17	0.222	0.22	65.211

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]
-0.251			-0.251		0.501

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.114
r_dihedral_angle_4_deg	21.23
r_dihedral_angle_3_deg	19.361
r_lrange_it	10.022
r_lrange_other	10.021
r_dihedral_angle_1_deg	8.557
r_scangle_it	7.36
r_scangle_other	7.359
r_mcangle_it	6.184
r_mcangle_other	6.183
r_scbond_it	4.996
r_scbond_other	4.854
r_mcbond_it	4.167
r_mcbond_other	4.166
r_angle_refined_deg	1.892
r_angle_other_deg	1.372
r_symmetry_nbd_refined	0.262
r_symmetry_xyhbond_nbd_refined	0.235
r_nbd_refined	0.21
r_symmetry_nbd_other	0.205
r_nbd_other	0.192
r_nbtor_refined	0.181
r_xyhbond_nbd_refined	0.168
r_symmetry_nbtor_other	0.088
r_chiral_restr	0.087
r_symmetry_xyhbond_nbd_other	0.063
r_bond_refined_d	0.013
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	5108
Nucleic Acid Atoms
Solvent Atoms	208
Heterogen Atoms	22

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing