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Galectin-1 in Complex with Methyl 6-fluoro-N-acetyllactosaminide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3T2T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 291 0.1M Tris-Cl, pH8, 0.2M lithium sulfate, 30% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.45 49.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.785 α = 90 b = 58.757 β = 90 c = 112.135 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 PIXEL DECTRIS PILATUS 6M 2021-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 1.631 35.017 95.3 0.118 0.998 10.62 9.2 35961 31.86
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.631 1.73 85.6 1.637 0.575 0.96 7.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.631 35.017 35957 1817 95.384 0.22 0.2181 0.2257 0.264 0.2714 31.414
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] 3.824 -2.975 -0.849
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.082 r_dihedral_angle_3_deg 12.778 r_lrange_it 8.09 r_lrange_other 8.089 r_dihedral_angle_1_deg 7.312 r_dihedral_angle_2_deg 6.41 r_scangle_it 6.279 r_scangle_other 6.277 r_mcangle_it 4.364 r_mcangle_other 4.364
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.082 r_dihedral_angle_3_deg 12.778 r_lrange_it 8.09 r_lrange_other 8.089 r_dihedral_angle_1_deg 7.312 r_dihedral_angle_2_deg 6.41 r_scangle_it 6.279 r_scangle_other 6.277 r_mcangle_it 4.364 r_mcangle_other 4.364 r_scbond_other 4.169 r_scbond_it 4.168 r_mcbond_it 2.974 r_mcbond_other 2.971 r_angle_refined_deg 1.771 r_angle_other_deg 0.564 r_nbd_other 0.255 r_nbd_refined 0.211 r_symmetry_nbd_other 0.209 r_symmetry_xyhbond_nbd_refined 0.178 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.17 r_symmetry_nbd_refined 0.136 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.077 r_symmetry_xyhbond_nbd_other 0.062 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2056 Nucleic Acid Atoms Solvent Atoms 207 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling