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Crystal structure of human galectin-9 N-terminal CRD in complex with N-acetyllactosamine trimer (crystal 2)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 293 0.1M TRI-SODIUM CITRATE (PH5.6), 1.0M MONO-AMMONIUM DEHYDRATE PHOSPHATE, pH 5.60, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.37 47.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.157 α = 90 b = 52.157 β = 90 c = 113.83 γ = 90
Symmetry Space Group P 41 21 2
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 210 2006-03-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.3 113.96 100 0.095 39617
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.35 100 0.506 9.7
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 (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 1.3 26.4 37638 1991 100 0.182 0.182 0.1808 0.192 0.1893 RANDOM 8.36
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] 0.15 0.15 -0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.118 r_dihedral_angle_4_deg 11.511 r_dihedral_angle_3_deg 9.773 r_dihedral_angle_1_deg 6.887 r_scangle_it 1.851 r_scbond_it 1.295 r_angle_refined_deg 1.221 r_mcangle_it 0.945 r_mcbond_it 0.547 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.118 r_dihedral_angle_4_deg 11.511 r_dihedral_angle_3_deg 9.773 r_dihedral_angle_1_deg 6.887 r_scangle_it 1.851 r_scbond_it 1.295 r_angle_refined_deg 1.221 r_mcangle_it 0.945 r_mcbond_it 0.547 r_nbtor_refined 0.314 r_nbd_refined 0.182 r_symmetry_vdw_refined 0.142 r_symmetry_hbond_refined 0.137 r_xyhbond_nbd_refined 0.102 r_chiral_restr 0.077 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 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 1132 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms 85
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling