6L68

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


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
2.6954.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.9α = 90
b = 48.9β = 90
c = 259.68γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU2018-11-30MSINGLE 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
11.9219.6197.70.99918.719.914791
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)
11.921.970.911

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-VALUE1QKQ1.9219.6071479174797.7140.1820.18040.209318.009
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]
0.0150.0070.015-0.048
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.643
r_dihedral_angle_4_deg20.763
r_dihedral_angle_3_deg13.495
r_dihedral_angle_1_deg8.319
r_lrange_other4.599
r_lrange_it4.592
r_scangle_it3.42
r_scangle_other3.418
r_scbond_it2.098
r_scbond_other2.098
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.643
r_dihedral_angle_4_deg20.763
r_dihedral_angle_3_deg13.495
r_dihedral_angle_1_deg8.319
r_lrange_other4.599
r_lrange_it4.592
r_scangle_it3.42
r_scangle_other3.418
r_scbond_it2.098
r_scbond_other2.098
r_mcangle_it1.924
r_mcangle_other1.923
r_angle_refined_deg1.469
r_mcbond_it1.228
r_mcbond_other1.22
r_angle_other_deg1.214
r_nbd_refined0.179
r_nbd_other0.173
r_symmetry_nbd_other0.164
r_symmetry_xyhbond_nbd_refined0.164
r_nbtor_refined0.159
r_xyhbond_nbd_refined0.094
r_symmetry_nbtor_other0.075
r_symmetry_nbd_refined0.072
r_chiral_restr0.063
r_bond_refined_d0.007
r_gen_planes_refined0.007
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1130
Nucleic Acid Atoms
Solvent Atoms60
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing