2FRG

Structure of the immunoglobulin-like domain of human TLT-1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1SMO	Hybrid model containing structurally conserved residues of TREM-1 (1SMO chain A), NKp44(1HKF), and D1 domain of polymeric immunoglobulin receptor (1XED chain E).
experimental model	PDB	1HKF	Hybrid model containing structurally conserved residues of TREM-1 (1SMO chain A), NKp44(1HKF), and D1 domain of polymeric immunoglobulin receptor (1XED chain E).
experimental model	PDB	1XED	Hybrid model containing structurally conserved residues of TREM-1 (1SMO chain A), NKp44(1HKF), and D1 domain of polymeric immunoglobulin receptor (1XED chain E).

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	293	Mother liquor contained 15-19% w/w PEG6000, 0.5M Na/K phosphate pH 5.6. Protein solution contained 10mg/ml TLT-1 in 20mM Tris pH 8. Protein and mother liquor were mixed in equal proportions at 15 C, and hanging drops were suspended over mother liquor., VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.095	α = 90
b = 79.981	β = 90
c = 25.78	γ = 90

Symmetry
Space Group	P 21 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	100	IMAGE PLATE	MARRESEARCH	mirrors	2005-05-24	M
2	1	x-ray	100	CCD	MARRESEARCH	monochromator	2005-06-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.54
2	SYNCHROTRON	APS BEAMLINE 22-ID	1.13	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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
2,1	1.19	30	98.2	0.064	25.9	6.4	32052	31487

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.19	1.23	87		0.31	3.2	3.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	Hybrid model containing structurally conserved residues of TREM-1 (1SMO chain A), NKp44(1HKF), and D1 domain of polymeric immunoglobulin receptor (1XED chain E).	1.19	30	31487	29945	1547	98.22	0.17711	0.17644	0.17	0.19062	0.18	RANDOM	13.076

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]
-0.28			0.35		-0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.03
r_dihedral_angle_4_deg	19.156
r_dihedral_angle_3_deg	13.118
r_dihedral_angle_1_deg	7.104
r_sphericity_free	6.914
r_scangle_it	4.236
r_scbond_it	3.067
r_sphericity_bonded	2.882
r_mcangle_it	2.11
r_rigid_bond_restr	1.766
r_mcbond_it	1.492
r_angle_refined_deg	1.452
r_nbtor_refined	0.31
r_nbd_refined	0.259
r_symmetry_vdw_refined	0.223
r_xyhbond_nbd_other	0.192
r_symmetry_hbond_refined	0.176
r_xyhbond_nbd_refined	0.162
r_chiral_restr	0.095
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	806
Nucleic Acid Atoms
Solvent Atoms	152
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
SCALEPACK	data scaling
PHASER	phasing