4ESK | pdb_00004esk

Crystal structure of a strand-swapped dimer of Mouse Leukocyte-associated immunoglobulin-like receptor 1 (NYSGRC-006047)IG-like domain

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4ETY	PDB ENTRY 4ETY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	Sitting Drop Vapor Diffusion	6	298	Protein (8.5mg/ml in 20 mM Trizma Base pH 8.2, 100 mM NaCl; Reservoir (1.0 M K/Na tartrate MES pH 6.0 - Wizard I & II #98); Cryoprotection (30% glycerol in Reservior solution), Sitting Drop Vapor Diffusion, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.141	α = 90
b = 73.121	β = 90
c = 90.609	γ = 90

Symmetry
Space Group	P 21 21 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	CCD	ADSC QUANTUM 315	MIRRORS	2011-10-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	1.0750	NSLS	X29A

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	1.76	38.51	97.5	0.043	59.3	14.5	41765	40723			18.1

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	1.76	1.79	85.8		0.363	6.7	13.5	1762

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	PDB ENTRY 4ETY	1.762	38.51	40637	2050	97.88	0.1853	0.1837	0.19	0.2161	0.22	RANDOM	20.6285

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			-0.42		0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.616
r_dihedral_angle_4_deg	15.286
r_dihedral_angle_3_deg	11.851
r_dihedral_angle_1_deg	6.352
r_angle_refined_deg	1.354
r_angle_other_deg	0.807
r_chiral_restr	0.086
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.616
r_dihedral_angle_4_deg	15.286
r_dihedral_angle_3_deg	11.851
r_dihedral_angle_1_deg	6.352
r_angle_refined_deg	1.354
r_angle_other_deg	0.807
r_chiral_restr	0.086
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3050
Nucleic Acid Atoms
Solvent Atoms	229
Heterogen Atoms	21

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	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.