6L6D

X-ray structure of human galectin-10 in complex with D-N-acetylgalactosamine


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2931.6 M ammonium sulfate, 0.1 M MES monohydrate pH 6.5, 10 % (v/v) 1,4-dioxane
Crystal Properties
Matthews coefficientSolvent content
2.7154.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.9α = 90
b = 48.9β = 90
c = 261.66γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU2019-08-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
11.9319.6399.80.99816.819.314992
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.931.980.903

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1QKQ1.9319.6281499275999.8140.2030.20170.233217.848
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]
0.0010.0010.001-0.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.522
r_dihedral_angle_4_deg22.931
r_dihedral_angle_3_deg17.407
r_dihedral_angle_1_deg9.076
r_lrange_it3.915
r_lrange_other3.915
r_scangle_it2.653
r_scangle_other2.651
r_mcangle_it1.78
r_mcangle_other1.779
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.522
r_dihedral_angle_4_deg22.931
r_dihedral_angle_3_deg17.407
r_dihedral_angle_1_deg9.076
r_lrange_it3.915
r_lrange_other3.915
r_scangle_it2.653
r_scangle_other2.651
r_mcangle_it1.78
r_mcangle_other1.779
r_scbond_it1.635
r_scbond_other1.634
r_angle_refined_deg1.363
r_angle_other_deg1.189
r_mcbond_it1.068
r_mcbond_other1.068
r_nbd_refined0.17
r_symmetry_nbd_other0.165
r_nbtor_refined0.159
r_symmetry_xyhbond_nbd_refined0.155
r_nbd_other0.154
r_xyhbond_nbd_refined0.12
r_symmetry_nbd_refined0.083
r_symmetry_nbtor_other0.073
r_chiral_restr0.057
r_bond_refined_d0.006
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1159
Nucleic Acid Atoms
Solvent Atoms70
Heterogen Atoms15

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing