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Crystal structure of human galectin-9 N-terminal CRD in complex with N-acetyllactosamine dimer (crystal 1)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.2 293 0.2M KF, 20% PEG 3350, pH 7.20, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.98 37.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.409 α = 90 b = 221.177 β = 90 c = 33.149 γ = 90
Symmetry Space Group P 21 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 315 2005-11-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A Photon Factory BL-5A
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 1.8 35 97.7 0.096 11.7 24085
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 1.8 1.86 90.8 0.242 9.2
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 1.8 35 23403 1253 97.5 0.198 0.196 0.1964 0.239 0.2402 RANDOM 25.64
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] 1.33 -1.98 0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.643 r_dihedral_angle_4_deg 16.141 r_dihedral_angle_1_deg 15.268 r_dihedral_angle_3_deg 13.269 r_scangle_it 3.912 r_scbond_it 2.606 r_mcangle_it 1.869 r_angle_refined_deg 1.807 r_mcbond_it 1.108 r_nbtor_refined 0.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.643 r_dihedral_angle_4_deg 16.141 r_dihedral_angle_1_deg 15.268 r_dihedral_angle_3_deg 13.269 r_scangle_it 3.912 r_scbond_it 2.606 r_mcangle_it 1.869 r_angle_refined_deg 1.807 r_mcbond_it 1.108 r_nbtor_refined 0.316 r_symmetry_hbond_refined 0.297 r_nbd_refined 0.197 r_symmetry_vdw_refined 0.183 r_xyhbond_nbd_refined 0.145 r_chiral_restr 0.128 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 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 2220 Nucleic Acid Atoms Solvent Atoms 182 Heterogen Atoms 102
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling