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Galectin-8N terminal domain in complex with Methyl 3-O-[3-O-benzyloxy]-malonyl-beta-D-galactopyranoside
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5T7S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298.15 0.1M sodium citrate dihydrate pH 5.6, 20% PEG 4000, 10% IPA
Crystal Properties Matthews coefficient Solvent content 2.23 44.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.391 α = 90 b = 40.003 β = 98.222 c = 70.324 γ = 90
Symmetry Space Group C 1 2 1
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 2019-03-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
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 1.59 46.32 99.9 0.116 0.997 8.8 6.8 41190
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.59 1.62 99.7 1.538 0.946 0.805 6.8
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 5T7S 1.59 46.31 41186 2139 99.91 0.194 0.1925 0.2014 0.2255 0.2333 19.814
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] -0.001 0.001 -0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.949 r_dihedral_angle_4_deg 20.393 r_dihedral_angle_3_deg 14.68 r_lrange_it 7.551 r_lrange_other 7.551 r_dihedral_angle_1_deg 7.176 r_scangle_it 4.561 r_scangle_other 4.56 r_scbond_it 3.023 r_scbond_other 3.022
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.949 r_dihedral_angle_4_deg 20.393 r_dihedral_angle_3_deg 14.68 r_lrange_it 7.551 r_lrange_other 7.551 r_dihedral_angle_1_deg 7.176 r_scangle_it 4.561 r_scangle_other 4.56 r_scbond_it 3.023 r_scbond_other 3.022 r_mcangle_other 2.584 r_mcangle_it 2.582 r_angle_refined_deg 1.837 r_mcbond_it 1.781 r_mcbond_other 1.774 r_angle_other_deg 1.405 r_chiral_restr_other 1.169 r_nbd_other 0.287 r_symmetry_nbd_refined 0.285 r_symmetry_xyhbond_nbd_refined 0.262 r_nbd_refined 0.223 r_symmetry_nbd_other 0.186 r_xyhbond_nbd_refined 0.173 r_nbtor_refined 0.168 r_chiral_restr 0.081 r_symmetry_nbtor_other 0.08 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2432 Nucleic Acid Atoms Solvent Atoms 138 Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing