1SYT

Crystal structure of signalling protein from goat SPG-40 in the presense of N,N',N''-triacetyl-chitotriose at 2.6A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1QZO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.829825mM Tris-HCl, 50mM NACl, 19% ethanol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.856

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.111α = 90
b = 66.036β = 90
c = 107.626γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298IMAGE PLATEMARRESEARCHMIRROR2004-01-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5414

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (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
12.62096.10.07411.58.71356313563
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.798.40.3763.1

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 REPLACEMENTTHROUGHOUT1QZO2.619.813563128926711000.182120.181430.179620.21703RANDOM35.73
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]
-0.27-0.020.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg19.652
r_scangle_it4.85
r_scbond_it2.971
r_dihedral_angle_1_deg2.605
r_mcangle_it2.538
r_angle_refined_deg1.725
r_mcbond_it1.353
r_angle_other_deg1.256
r_symmetry_vdw_other0.26
r_nbd_refined0.252
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg19.652
r_scangle_it4.85
r_scbond_it2.971
r_dihedral_angle_1_deg2.605
r_mcangle_it2.538
r_angle_refined_deg1.725
r_mcbond_it1.353
r_angle_other_deg1.256
r_symmetry_vdw_other0.26
r_nbd_refined0.252
r_nbd_other0.243
r_xyhbond_nbd_other0.177
r_nbtor_other0.157
r_xyhbond_nbd_refined0.143
r_chiral_restr0.129
r_symmetry_vdw_refined0.121
r_symmetry_hbond_refined0.115
r_bond_refined_d0.019
r_gen_planes_refined0.007
r_gen_planes_other0.005
r_bond_other_d0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2874
Nucleic Acid Atoms
Solvent Atoms204
Heterogen Atoms39

Software

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