3SCM | pdb_00003scm

Crystal structure of autoreactive-Valpha14-Vbeta6 NKT TCR in complex with CD1d-isoglobotrihexosylceramide

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.2	293	0.1M Sodium citrate, 14% PEG 6000, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.38	63.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.523	α = 90
b = 94.523	β = 90
c = 289.613	γ = 90

Symmetry
Space Group	P 41 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	193	CCD	ADSC QUANTUM 315r		2011-03-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	1.47	Australian Synchrotron	MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	94.52	100	0.159	6.5	6.3	45523	45523	1	1	64.8

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	2.5	89.86	45484	2301	97.75	0.2749	0.2726	0.2648	0.3183	0.3088	RANDOM	56.23

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]
-0.06			-0.06		0.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.24
r_dihedral_angle_4_deg	16.379
r_dihedral_angle_3_deg	15.844
r_dihedral_angle_1_deg	5.696
r_mcangle_it	2.493
r_mcbond_it	1.79
r_angle_refined_deg	1.398
r_scangle_it	1.248
r_scbond_it	0.708
r_chiral_restr	0.076

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.24
r_dihedral_angle_4_deg	16.379
r_dihedral_angle_3_deg	15.844
r_dihedral_angle_1_deg	5.696
r_mcangle_it	2.493
r_mcbond_it	1.79
r_angle_refined_deg	1.398
r_scangle_it	1.248
r_scbond_it	0.708
r_chiral_restr	0.076
r_bond_refined_d	0.013
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6516
Nucleic Acid Atoms
Solvent Atoms	129
Heterogen Atoms	135

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.