6L64

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


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
2.6653.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.65α = 90
b = 48.65β = 90
c = 259.23γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU2018-12-06MSINGLE 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
12.0819.5299.80.99815.119.411869
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)
12.082.130.9034.1

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-VALUE1QKQ2.0819.5171186956499.7730.20.19870.235722.369
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]
0.0010.001-0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.897
r_dihedral_angle_4_deg20.076
r_dihedral_angle_3_deg16.116
r_dihedral_angle_1_deg9.395
r_lrange_it4.742
r_lrange_other4.568
r_scangle_it3.321
r_scangle_other3.32
r_scbond_it2.105
r_scbond_other2.104
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.897
r_dihedral_angle_4_deg20.076
r_dihedral_angle_3_deg16.116
r_dihedral_angle_1_deg9.395
r_lrange_it4.742
r_lrange_other4.568
r_scangle_it3.321
r_scangle_other3.32
r_scbond_it2.105
r_scbond_other2.104
r_mcangle_it1.965
r_mcangle_other1.964
r_angle_refined_deg1.539
r_mcbond_it1.263
r_mcbond_other1.263
r_angle_other_deg1.159
r_nbd_refined0.185
r_nbd_other0.184
r_symmetry_nbd_other0.162
r_nbtor_refined0.162
r_symmetry_xyhbond_nbd_refined0.15
r_symmetry_nbd_refined0.106
r_xyhbond_nbd_refined0.1
r_symmetry_nbtor_other0.073
r_chiral_restr0.058
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 Atoms1124
Nucleic Acid Atoms
Solvent Atoms30
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing