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Structure of human Galectin-3 CRD in complex with TD-139 belonging to P31 space group.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZSL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 28-35% PEG 4000/6000, 0.1M Tris (pH 7.5 - pH 8.5), 0.1M MgCl2, 0.4M NaSCN
Crystal Properties Matthews coefficient Solvent content 1.98 37.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.843 α = 90 b = 40.843 β = 90 c = 152.631 γ = 120
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 RAYONIX MX-300 2014-09-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.9795 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.97 50 99.7 0.063 12.2 4.3 20163
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.97 2.04 100 0.738 4.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3ZSL 1.97 32.09 19011 1119 99.62 0.2042 0.2022 0.2022 0.2351 0.2356 RANDOM 62.585
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] 20.71 20.71 -41.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.92 r_dihedral_angle_3_deg 18.262 r_dihedral_angle_4_deg 6.846 r_dihedral_angle_1_deg 5.328 r_angle_refined_deg 1.431 r_angle_other_deg 0.63 r_chiral_restr 0.108 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_gen_planes_other 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.92 r_dihedral_angle_3_deg 18.262 r_dihedral_angle_4_deg 6.846 r_dihedral_angle_1_deg 5.328 r_angle_refined_deg 1.431 r_angle_other_deg 0.63 r_chiral_restr 0.108 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_gen_planes_other 0.001 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2134 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms 152
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing