6L6A

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


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
2.754.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.83α = 90
b = 48.83β = 90
c = 260.94γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU2018-10-02MSINGLE 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
11.8119.34980.99723.119.217615
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)
11.811.860.918

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-VALUE1QKQ1.8119.3381761590898.0410.190.18860.222216.726
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]
-0.004-0.002-0.0040.012
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.9
r_dihedral_angle_4_deg23.579
r_dihedral_angle_3_deg14.198
r_dihedral_angle_1_deg9.076
r_lrange_it4.193
r_lrange_other4.162
r_scangle_it3.121
r_scangle_other3.119
r_scbond_it1.986
r_scbond_other1.986
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.9
r_dihedral_angle_4_deg23.579
r_dihedral_angle_3_deg14.198
r_dihedral_angle_1_deg9.076
r_lrange_it4.193
r_lrange_other4.162
r_scangle_it3.121
r_scangle_other3.119
r_scbond_it1.986
r_scbond_other1.986
r_mcangle_it1.712
r_mcangle_other1.711
r_angle_refined_deg1.442
r_angle_other_deg1.271
r_mcbond_other1.071
r_mcbond_it1.07
r_nbd_other0.177
r_nbd_refined0.175
r_symmetry_nbd_other0.168
r_nbtor_refined0.162
r_symmetry_nbd_refined0.126
r_symmetry_xyhbond_nbd_refined0.125
r_xyhbond_nbd_refined0.092
r_symmetry_nbtor_other0.074
r_chiral_restr0.072
r_bond_refined_d0.007
r_gen_planes_refined0.007
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 Atoms85
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing