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

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2DPE 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.8298Tri-HCl, 20% Ethanol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.6253.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.873α = 90
b = 66.415β = 90
c = 105.692γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayIMAGE PLATEMAR scanner 345 mm plateMirror2007-03-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X13EMBL/DESY, HAMBURGX13

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.6555.999.95213550988
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.651.6899.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2DPE1.6555.95213550988107599.90.182110.168390.167460.21725RANDOM24.215
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]
-0.06-0.070.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.608
r_dihedral_angle_1_deg4.88
r_scangle_it4.049
r_scbond_it2.492
r_mcangle_it1.665
r_angle_refined_deg1.507
r_mcbond_it0.907
r_symmetry_vdw_refined0.408
r_symmetry_hbond_refined0.269
r_nbd_refined0.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.608
r_dihedral_angle_1_deg4.88
r_scangle_it4.049
r_scbond_it2.492
r_mcangle_it1.665
r_angle_refined_deg1.507
r_mcbond_it0.907
r_symmetry_vdw_refined0.408
r_symmetry_hbond_refined0.269
r_nbd_refined0.23
r_xyhbond_nbd_refined0.134
r_chiral_restr0.113
r_bond_refined_d0.013
r_gen_planes_refined0.006
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 AtomsNumber
Protein Atoms2878
Nucleic Acid Atoms
Solvent Atoms586
Heterogen Atoms86

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing