4Z78 | pdb_00004z78

Weak TCR binding to an unstable insulin epitope drives type 1 diabetes

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		291	4% PEG 4000, 0.1 M sodium acetate pH 4.6

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.17	α = 90
b = 151.57	β = 90
c = 182.23	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315r		2012-02-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9173	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	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	2.304	182.23	100	0.127	0.148	0.055	10.4	7.2	57725	57725

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.36	100		0.929	0.929	0.399	0.8	7.3	4165

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	2.304	78.09	54718	2925	99.96	0.1904	0.1882	0.1927	0.2327	0.2351	RANDOM	39.766

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]
-2.14			0.67		1.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.56
r_dihedral_angle_4_deg	20.36
r_dihedral_angle_3_deg	18.029
r_dihedral_angle_1_deg	6.879
r_mcangle_it	2.54
r_angle_refined_deg	1.744
r_mcbond_it	1.546
r_mcbond_other	1.546
r_angle_other_deg	1.214
r_chiral_restr	0.108
r_bond_refined_d	0.015
r_gen_planes_refined	0.009
r_bond_other_d	0.006
r_gen_planes_other	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9615
Nucleic Acid Atoms
Solvent Atoms	364
Heterogen Atoms	101

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction