6TF7

Human galectin-3c in complex with a galactose derivative


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ZSL 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP30020 MG/ML GALECTIN-3C, 100MM NACL, 30 % W/V PEG 4000, 0.4 M NASCN, 10 MM BETA-MERCAPTOETHANOL, 10 MM PHOSHATE, 100 MM MGCL2, 100 MM TRIS/HCL PH 7.5, 4.5 MM LIGAND
Crystal Properties
Matthews coefficientSolvent content
2.141.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.14α = 90
b = 58.16β = 90
c = 62.84γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2014-03-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-21.03841MAX III911-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.429.0899.60.048245.826601
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.440.519

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3ZSL1.429.0825271133099.650.13740.13480.1872RANDOM14.598
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]
-0.650.270.38
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free56.871
r_dihedral_angle_2_deg34.563
r_dihedral_angle_3_deg12.337
r_sphericity_bonded11.722
r_dihedral_angle_4_deg8.881
r_dihedral_angle_1_deg7.984
r_rigid_bond_restr4.58
r_angle_refined_deg2.184
r_angle_other_deg1.65
r_chiral_restr0.169
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free56.871
r_dihedral_angle_2_deg34.563
r_dihedral_angle_3_deg12.337
r_sphericity_bonded11.722
r_dihedral_angle_4_deg8.881
r_dihedral_angle_1_deg7.984
r_rigid_bond_restr4.58
r_angle_refined_deg2.184
r_angle_other_deg1.65
r_chiral_restr0.169
r_bond_refined_d0.019
r_gen_planes_refined0.012
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1109
Nucleic Acid Atoms
Solvent Atoms174
Heterogen Atoms45

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
REFMACphasing