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Crystal structure of mouse galectin-9 N-terminal CRD in complex with lactose
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 2.1 41.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.643 α = 90 b = 58.472 β = 90 c = 92 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 CCD ADSC QUANTUM 315 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 0.9780 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 1.6 50 93.7 0.088 38497
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) 1.6 1.66 98 0.345
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 1.6 49.39 36422 1958 93.52 0.18513 0.18255 0.1827 0.23197 0.2323 RANDOM 16.102
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] -0.65 -0.21 0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.655 r_dihedral_angle_3_deg 11.71 r_dihedral_angle_4_deg 10.691 r_dihedral_angle_1_deg 6.811 r_scangle_it 3.554 r_scbond_it 2.292 r_angle_refined_deg 1.438 r_mcangle_it 1.376 r_mcbond_it 0.882 r_nbtor_refined 0.318
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.655 r_dihedral_angle_3_deg 11.71 r_dihedral_angle_4_deg 10.691 r_dihedral_angle_1_deg 6.811 r_scangle_it 3.554 r_scbond_it 2.292 r_angle_refined_deg 1.438 r_mcangle_it 1.376 r_mcbond_it 0.882 r_nbtor_refined 0.318 r_symmetry_vdw_refined 0.214 r_nbd_refined 0.207 r_symmetry_hbond_refined 0.178 r_xyhbond_nbd_refined 0.168 r_chiral_restr 0.103 r_bond_refined_d 0.011 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 2422 Nucleic Acid Atoms Solvent Atoms 699 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing