6CXE | pdb_00006cxe

Structure of alpha-GSA[26,6P] bound by CD1d and in complex with the Va14Vb8.2 TCR

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3QUZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.1	295	16% PEG 3350, 0.06M Citric acid, 0.04M BIS-TRIS propane pH 4.1

Crystal Properties
Matthews coefficient	Solvent content
2.96	58.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.437	α = 90
b = 189.071	β = 90
c = 150.908	γ = 90

Symmetry
Space Group	C 2 2 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	PIXEL	DECTRIS PILATUS 6M		2016-11-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.98	SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.05	50	96.7	0.078	0.086	0.035	8.4	5.8		67704

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	2.05	2.12	87.9		0.464	0.515	0.218	0.879		5.1

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 (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	3QUZ	2.05	50	66292	1388	95.9	0.2096	0.2088	0.21	0.2481	0.25	RANDOM	49.466

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]
-1.61			4.11		-2.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.321
r_dihedral_angle_4_deg	17.072
r_dihedral_angle_3_deg	15.38
r_dihedral_angle_1_deg	6.314
r_angle_refined_deg	1.311
r_chiral_restr	0.081
r_bond_refined_d	0.009
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6375
Nucleic Acid Atoms
Solvent Atoms	279
Heterogen Atoms	134

Software

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

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.