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Crystal structure of the human galectin-7 in complex with p-Methoxyphenyl 3-O-benzyl-beta-D-galactopyranoside
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OY8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 100 mM MgCl2, 100 mM HEPES pH 7, 19% PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.99 38.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.255 α = 90 b = 64.894 β = 90 c = 70.392 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 2025-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1 ELETTRA 11.2C
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 1.9 35.56 92.81 1 39.22 10.6 18413
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 1.9 1.968 0.984
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 (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 1.9 35.56 17410 1003 92.85 0.20612 0.20423 0.2134 0.23598 0.2316 RANDOM 31.148
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] -1.28 0.36 0.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.859 r_dihedral_angle_2_deg 9.212 r_long_range_B_other 8.127 r_long_range_B_refined 8.121 r_dihedral_angle_1_deg 7.503 r_scangle_other 5.889 r_mcangle_it 4.003 r_mcangle_other 4.003 r_scbond_it 3.823 r_scbond_other 3.822
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.859 r_dihedral_angle_2_deg 9.212 r_long_range_B_other 8.127 r_long_range_B_refined 8.121 r_dihedral_angle_1_deg 7.503 r_scangle_other 5.889 r_mcangle_it 4.003 r_mcangle_other 4.003 r_scbond_it 3.823 r_scbond_other 3.822 r_mcbond_it 2.879 r_mcbond_other 2.878 r_angle_refined_deg 1.612 r_angle_other_deg 0.539 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2074 Nucleic Acid Atoms Solvent Atoms 113 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction