6L6B

X-ray structure of human galectin-10 in complex with L-fucose


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
2.754.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.82α = 90
b = 48.82β = 90
c = 261.03γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU2018-10-05MSINGLE 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
11.819.5599.50.99715.118.618129
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)
11.81.850.977

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-VALUE1QKQ1.80219.5461812992699.5440.2150.21260.255316.868
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]
0.0460.0230.046-0.148
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.19
r_dihedral_angle_4_deg19.101
r_dihedral_angle_3_deg14.607
r_dihedral_angle_1_deg9.106
r_lrange_it3.625
r_lrange_other3.617
r_scangle_it2.396
r_scangle_other2.394
r_mcangle_it1.595
r_mcangle_other1.594
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.19
r_dihedral_angle_4_deg19.101
r_dihedral_angle_3_deg14.607
r_dihedral_angle_1_deg9.106
r_lrange_it3.625
r_lrange_other3.617
r_scangle_it2.396
r_scangle_other2.394
r_mcangle_it1.595
r_mcangle_other1.594
r_scbond_it1.484
r_scbond_other1.483
r_angle_refined_deg1.419
r_angle_other_deg1.21
r_mcbond_it0.982
r_mcbond_other0.982
r_nbd_refined0.171
r_symmetry_nbd_other0.162
r_nbtor_refined0.16
r_nbd_other0.157
r_symmetry_xyhbond_nbd_refined0.151
r_xyhbond_nbd_refined0.128
r_symmetry_nbd_refined0.098
r_symmetry_nbtor_other0.074
r_chiral_restr0.072
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 Atoms74
Heterogen Atoms11

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing