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Crystal structure of mouse galectin-9 N-terminal CRD in complex with N-acetyllactosamine dimer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1A3K PDB entry 1A3K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 289 5% PEG6000, 0.1M citrate (pH5.0), VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.12 42.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.796 α = 90 b = 94.422 β = 90 c = 56.544 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD ADSC QUANTUM 315 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
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 1.78 56.52 99.8 0.058 15123
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 (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 PDB entry 1A3K 1.78 56.52 14364 758 99.71 0.18245 0.18077 0.1795 0.21203 0.211 RANDOM 24.327
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] 0.16 1.91 -2.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.443 r_dihedral_angle_3_deg 14.352 r_dihedral_angle_4_deg 8.737 r_dihedral_angle_1_deg 6.993 r_scangle_it 3.901 r_scbond_it 2.437 r_mcangle_it 1.552 r_angle_refined_deg 1.459 r_mcbond_it 1.007 r_symmetry_vdw_refined 0.334
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.443 r_dihedral_angle_3_deg 14.352 r_dihedral_angle_4_deg 8.737 r_dihedral_angle_1_deg 6.993 r_scangle_it 3.901 r_scbond_it 2.437 r_mcangle_it 1.552 r_angle_refined_deg 1.459 r_mcbond_it 1.007 r_symmetry_vdw_refined 0.334 r_nbtor_refined 0.317 r_symmetry_hbond_refined 0.236 r_nbd_refined 0.222 r_xyhbond_nbd_refined 0.141 r_chiral_restr 0.105 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1211 Nucleic Acid Atoms Solvent Atoms 132 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing