4ETY | pdb_00004ety

Crystal structure of a strand-swapped dimer of Mouse Leukocyte-associated immunoglobulin-like receptor 1 (NYSGRC-006047) Extra Cellular Domain

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		SAD model built using Phenix AutoSol wizard

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	Sitting Drop Vapor Diffusion	5.5	298	Protein preparation by Refolding. Protein (11.5mg/ml in 20 mM Trizma Base pH 8.0, 100 mM NaCl; Reservoir ( 0.2 M Sodium chloride, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350; Index HR F10); Cryoprotection (30% Ethylene glycol in Reservior solution), Sitting Drop Vapor Diffusion, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 175.588	α = 90
b = 57.427	β = 105.15
c = 47.795	γ = 90

Symmetry
Space Group	C 1 2 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	RAYONIX MX225HE	MIRRORS	2011-11-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.9793	APS	31-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
1	1.9	50	99	0.103	13.6	7	36280	36066			19.7

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	1.9	1.93	98.8		0.946		6.8	1742

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	SAD	THROUGHOUT	Built using Phenix AutoSol wizard	1.9	27.81	36066	1798	99.07	0.2017	0.2003	0.2138	0.2278	0.2335	RANDOM	33.5637

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]
-1.37		0.17	2.39		-0.93

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.159
r_dihedral_angle_4_deg	14.486
r_dihedral_angle_3_deg	11.431
r_dihedral_angle_1_deg	6.719
r_angle_refined_deg	1.45
r_angle_other_deg	0.781
r_chiral_restr	0.086
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2993
Nucleic Acid Atoms
Solvent Atoms	94
Heterogen Atoms	40

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing