2PI6

Crystal structure of the sheep signalling glycoprotein (SPS-40) complex with 2-methyl-2-4-pentanediol at 1.65A resolution reveals specific binding characteristics of SPS-40

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2DPE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.8	298	Tri-HCl, 20% Ethanol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.62	53.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.873	α = 90
b = 66.415	β = 90
c = 105.692	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		IMAGE PLATE	MAR scanner 345 mm plate	Mirror	2007-03-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13		EMBL/DESY, HAMBURG	X13

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.65	55.9	99.9			52135	50988

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.65	1.68	99.7

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2DPE	1.65	55.9	52135	50988	1075	99.9	0.18211	0.16839	0.16746	0.21725	RANDOM	24.215

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]
-0.06			-0.07		0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.608
r_dihedral_angle_1_deg	4.88
r_scangle_it	4.049
r_scbond_it	2.492
r_mcangle_it	1.665
r_angle_refined_deg	1.507
r_mcbond_it	0.907
r_symmetry_vdw_refined	0.408
r_symmetry_hbond_refined	0.269
r_nbd_refined	0.23
r_xyhbond_nbd_refined	0.134
r_chiral_restr	0.113
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2878
Nucleic Acid Atoms
Solvent Atoms	586
Heterogen Atoms	86

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing