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Crystal structure of galectin-3 CRD in complex with galactopentaose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZSK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 19 mg/ml Gal3C in 10 mM sodium phosphate buffer pH 7.5, 100 mM NaCl, 10 mM beta-mercaptoethanol, 0.02 % NaN3. 3.5 microlitres Gal3C were mixed with 3.5 microlitres 100 mM galactopentaose solution and incubated on ice for one hour. Crystals were obtained in 30% w/v PEG 4000, 0.1 M Tris/HCl pH 7.5, 0.1M MgCl2, 0.4M NaSCN, 8 mM beta-mercaptoethanol. Cryoprotectant contained an additional 11% glycerol.
Crystal Properties Matthews coefficient Solvent content 2.19 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.06 α = 90 b = 58.2 β = 90 c = 62.99 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD FOCUSING MIRRORS 2013-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-3 1.0000 MAX II I911-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.41 27.7 98.2 0.053 0.999 19.8 5.9 25876 19.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.41 1.49 90.2 0.351 0.885 4.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 3ZSK 1.41 27.699 1.36 25842 1290 98.43 0.1183 0.1164 0.1316 0.1533 0.162
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.976 f_angle_d 1.24 f_chiral_restr 0.074 f_plane_restr 0.006 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1109 Nucleic Acid Atoms Solvent Atoms 217 Heterogen Atoms 23
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling REFMAC refinement