Experiment: 4Y4F

Crystal structure of the mCD1d/GCK127/iNKTCR ternary complex

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Q7Y	2Q7Y, 3QUZ
experimental model	PDB	3QUZ	2Q7Y, 3QUZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295.5	17% PEG 4000, 0.2M potassium acetate

Crystal Properties
Matthews coefficient	Solvent content
3.24	62.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.589	α = 90
b = 149.728	β = 96.46
c = 101.386	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	ADSC QUANTUM 315r		2011-01-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1	1.0	SSRL	BL7-1

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	3.19	40	98.2	0.13	13.7	3.3		38286			80.27

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.19	3.31	91.1		0.639	2.07	3.3

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	2Q7Y, 3QUZ	3.19	35.09	37072	1190	98.51	0.2194	0.2181	0.2172	0.2574	0.2575	RANDOM	87.411

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]
0.03		0.07	-0.02		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.876
r_dihedral_angle_3_deg	13.428
r_dihedral_angle_4_deg	11.059
r_dihedral_angle_1_deg	4.603
r_angle_refined_deg	0.879
r_chiral_restr	0.053
r_bond_refined_d	0.006
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12384
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	210

Software

Software
Software Name	Purpose
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing
Coot	model building
REFMAC	refinement
PDB_EXTRACT	data extraction