2GYS | pdb_00002gys

2.7 A structure of the extracellular domains of the human beta common receptor involved in IL-3, IL-5, and GM-CSF signalling

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GH7	pdb entry 1gh7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.4	277	10% polyethylene glycol 5000 mono-methyl ether in phosphate buffer, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.47	64.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 184.909	α = 90
b = 184.909	β = 90
c = 101.047	γ = 120

Symmetry
Space Group	H 3

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	MAR CCD 165 mm		2004-11-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-ID-B	1.117	APS	14-ID-B

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	2.7	50	91.4	0.06	19.2	5.96	35381	32327			45.3

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	2.7	2.8	40.2		0.153	2.4

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 (All)	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	FOURIER SYNTHESIS	THROUGHOUT	pdb entry 1gh7	2.7	50	35381	30934	1392	91.36	0.21426	0.21426	0.21169	0.21	0.26913	0.27	RANDOM	51.114

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]
-1.16	-0.58		-1.16		1.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.832
r_dihedral_angle_3_deg	22.321
r_dihedral_angle_4_deg	21.065
r_dihedral_angle_1_deg	8.299
r_scangle_it	3.557
r_angle_refined_deg	2.217
r_scbond_it	2.171
r_mcangle_it	1.35
r_mcbond_it	0.75
r_nbtor_refined	0.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.832
r_dihedral_angle_3_deg	22.321
r_dihedral_angle_4_deg	21.065
r_dihedral_angle_1_deg	8.299
r_scangle_it	3.557
r_angle_refined_deg	2.217
r_scbond_it	2.171
r_mcangle_it	1.35
r_mcbond_it	0.75
r_nbtor_refined	0.33
r_symmetry_hbond_refined	0.31
r_nbd_refined	0.254
r_symmetry_vdw_refined	0.218
r_chiral_restr	0.167
r_xyhbond_nbd_refined	0.164
r_bond_refined_d	0.022
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6280
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	174

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
CCP4	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.