5T7S

Crystal structure of galectin-8N in complex with Lactose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3AP5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29310 mM sodium phosphate, 137 mM sodium chloride, 2.7 mM potassium chloride, 1.8 mM potassium phosphate
Crystal Properties
Matthews coefficientSolvent content
2.3848.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.61α = 90
b = 50.4β = 90
c = 69.73γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2015-10-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX10.9537Australian SynchrotronMX1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.940.851000.059248.613910

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3AP51.940.851319867099.970.152130.150690.17962RANDOM16.843
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]
-0.02-0.010.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.369
r_dihedral_angle_4_deg14.785
r_dihedral_angle_3_deg10.789
r_long_range_B_other8.34
r_long_range_B_refined8.321
r_dihedral_angle_1_deg6.619
r_scangle_other5.672
r_scbond_it3.646
r_scbond_other3.595
r_mcangle_other2.488
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.369
r_dihedral_angle_4_deg14.785
r_dihedral_angle_3_deg10.789
r_long_range_B_other8.34
r_long_range_B_refined8.321
r_dihedral_angle_1_deg6.619
r_scangle_other5.672
r_scbond_it3.646
r_scbond_other3.595
r_mcangle_other2.488
r_mcangle_it2.477
r_mcbond_it1.857
r_mcbond_other1.831
r_angle_refined_deg1.254
r_angle_other_deg0.808
r_chiral_restr0.075
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1178
Nucleic Acid Atoms
Solvent Atoms222
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing