6L67

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


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
2.6753.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.66α = 90
b = 48.66β = 90
c = 259.8γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU2018-12-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

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
11.9719.5397.10.99918.120.113537
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)
11.972.020.916

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-VALUE1QKQ1.9719.5261353766897.0950.1960.1950.224825.772
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]
-0.102-0.051-0.1020.332
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.879
r_dihedral_angle_3_deg14.925
r_dihedral_angle_4_deg14.54
r_dihedral_angle_1_deg9.527
r_lrange_other5.42
r_lrange_it5.417
r_scangle_it3.923
r_scangle_other3.923
r_mcangle_it2.714
r_mcangle_other2.713
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.879
r_dihedral_angle_3_deg14.925
r_dihedral_angle_4_deg14.54
r_dihedral_angle_1_deg9.527
r_lrange_other5.42
r_lrange_it5.417
r_scangle_it3.923
r_scangle_other3.923
r_mcangle_it2.714
r_mcangle_other2.713
r_scbond_it2.487
r_scbond_other2.477
r_mcbond_it1.724
r_mcbond_other1.719
r_angle_refined_deg1.477
r_angle_other_deg1.161
r_nbd_other0.189
r_nbd_refined0.167
r_nbtor_refined0.161
r_symmetry_nbd_other0.159
r_symmetry_nbd_refined0.127
r_symmetry_xyhbond_nbd_refined0.108
r_xyhbond_nbd_refined0.096
r_symmetry_nbtor_other0.072
r_chiral_restr0.057
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 Atoms1151
Nucleic Acid Atoms
Solvent Atoms43
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing