3RQ3 | pdb_00003rq3

Structure of T-cell immunoreceptor with immunoglobulin and ITIM domains (TIGIT) in hexagonal crystal form

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3Q0H

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	298	1.0M Ammonium Sulfate, 0.1M BIS-TRIS pH 5.5, 1% PEG3350, Vapor diffusion, Sitting drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.96	68.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 118.614	α = 90
b = 118.614	β = 90
c = 98.197	γ = 120

Symmetry
Space Group	P 64 2 2

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 315		2010-09-23		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	0.9793	NSLS	X29A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.7	37.8	100	0.085	0.061	10	13.7	11650	11650

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.7	2.75	100			13.9	555

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	3Q0H	2.7	37.82	11255	536	96.75	0.2082	0.2059	0.2	0.2531	0.25	RANDOM	40.8379

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]
-0.25	-0.12		-0.25		0.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.597
r_dihedral_angle_3_deg	20.01
r_dihedral_angle_4_deg	15.157
r_dihedral_angle_1_deg	8.462
r_scangle_it	3.866
r_scbond_it	2.414
r_angle_refined_deg	1.852
r_mcangle_it	1.641
r_mcbond_it	0.862
r_chiral_restr	0.109

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.597
r_dihedral_angle_3_deg	20.01
r_dihedral_angle_4_deg	15.157
r_dihedral_angle_1_deg	8.462
r_scangle_it	3.866
r_scbond_it	2.414
r_angle_refined_deg	1.852
r_mcangle_it	1.641
r_mcbond_it	0.862
r_chiral_restr	0.109
r_bond_refined_d	0.019
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1636
Nucleic Acid Atoms
Solvent Atoms	38
Heterogen Atoms	1

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
MOLREP	phasing

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.