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Crystal structure of human galectin-3 CRD in complex with selenodigalactoside
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6B8K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 297 31% PEG 3100, 100 mM tris-HCl pH 7.5, 100 mM MgCl2, 8 mM 2-Mercaptoethanol
Crystal Properties Matthews coefficient Solvent content 2.13 42.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.411 α = 90 b = 58.034 β = 90 c = 63.531 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 ADSC QUANTUM 210 2016-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.9737 Australian Synchrotron MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.959 30.862 91.3 0.999 20.54 4.2 9287
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.96 2.03 0.944 5.45
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6B8K 1.96 30.86 9287 469 91.389 0.152 0.1501 0.1605 0.183 0.1909 17.161
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] -0.002 0.001 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.653 r_dihedral_angle_3_deg 12.658 r_dihedral_angle_4_deg 11.471 r_dihedral_angle_1_deg 8.157 r_lrange_it 5.439 r_lrange_other 5.434 r_scangle_it 3.971 r_scangle_other 3.969 r_mcangle_it 2.668 r_mcangle_other 2.668
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.653 r_dihedral_angle_3_deg 12.658 r_dihedral_angle_4_deg 11.471 r_dihedral_angle_1_deg 8.157 r_lrange_it 5.439 r_lrange_other 5.434 r_scangle_it 3.971 r_scangle_other 3.969 r_mcangle_it 2.668 r_mcangle_other 2.668 r_scbond_it 2.461 r_scbond_other 2.459 r_mcbond_it 1.68 r_mcbond_other 1.671 r_angle_refined_deg 1.629 r_angle_other_deg 1.311 r_nbd_refined 0.202 r_symmetry_nbd_other 0.17 r_nbtor_refined 0.157 r_nbd_other 0.152 r_xyhbond_nbd_refined 0.114 r_symmetry_xyhbond_nbd_refined 0.096 r_symmetry_nbd_refined 0.09 r_chiral_restr 0.079 r_symmetry_nbtor_other 0.075 r_chiral_restr_other 0.039 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1112 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing