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Co-crystallization of human galectin-3 CRD complex with Methyl 2-O-(2-nitro-4-chloro)-benzoyl-3-O-toluoyl-b-D-talopyranoside
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NMO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 100 mM Tris-HCl, pH 7.0, 100 mM MgCl2, 31-35 % w/v polyethylene glycol 6000
Crystal Properties Matthews coefficient Solvent content 2.06 40.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.201 α = 90 b = 57.814 β = 90 c = 62.098 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 315r 2013-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.9537 Australian Synchrotron MX1
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 1.05 31.27 99.9 0.043 24.1 7.6 61577
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 1.05 1.07 0.346 3.9
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 2NMO 1.05 30.701 61505 3070 99.904 0.157 0.1566 0.1625 0.1733 0.1801 8.985
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] 0.114 -0.133 0.019
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.201 r_dihedral_angle_4_deg 13.209 r_dihedral_angle_3_deg 10.109 r_dihedral_angle_1_deg 7.65 r_lrange_it 4.477 r_lrange_other 4.476 r_scangle_it 2.476 r_scangle_other 2.474 r_angle_refined_deg 1.981 r_mcangle_it 1.781
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.201 r_dihedral_angle_4_deg 13.209 r_dihedral_angle_3_deg 10.109 r_dihedral_angle_1_deg 7.65 r_lrange_it 4.477 r_lrange_other 4.476 r_scangle_it 2.476 r_scangle_other 2.474 r_angle_refined_deg 1.981 r_mcangle_it 1.781 r_mcangle_other 1.781 r_scbond_it 1.667 r_scbond_other 1.664 r_angle_other_deg 1.485 r_mcbond_it 1.131 r_mcbond_other 1.131 r_symmetry_xyhbond_nbd_refined 0.298 r_nbd_refined 0.247 r_xyhbond_nbd_refined 0.224 r_nbd_other 0.188 r_symmetry_nbd_other 0.179 r_nbtor_refined 0.177 r_symmetry_nbd_refined 0.156 r_chiral_restr 0.11 r_symmetry_nbtor_other 0.085 r_bond_refined_d 0.018 r_chiral_restr_other 0.014 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1109 Nucleic Acid Atoms Solvent Atoms 205 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing