☰ Navigation Tabs
Crystal structure of mouse galectin-9 N-terminal CRD (crystal form 1)
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 9.5 289 15% ethanol, 0.1M CHES (pH9.5), VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.57 52.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.094 α = 90 b = 58.094 β = 90 c = 221.682 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 90 CCD ADSC QUANTUM 4 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A 1.0000 Photon Factory BL-6A
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 2.5 50 99.9 0.072 35 14051
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) 2.5 2.59 100 0.352 7.3
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 2.5 35.25 13283 696 99.99 0.20822 0.20446 0.2039 0.28333 0.2827 RANDOM 28.563
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] 0.14 0.14 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.912 r_dihedral_angle_3_deg 16.869 r_dihedral_angle_4_deg 14.985 r_dihedral_angle_1_deg 7.885 r_scangle_it 3.346 r_scbond_it 2.129 r_angle_other_deg 1.709 r_angle_refined_deg 1.595 r_mcangle_it 1.587 r_mcbond_it 0.838
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.912 r_dihedral_angle_3_deg 16.869 r_dihedral_angle_4_deg 14.985 r_dihedral_angle_1_deg 7.885 r_scangle_it 3.346 r_scbond_it 2.129 r_angle_other_deg 1.709 r_angle_refined_deg 1.595 r_mcangle_it 1.587 r_mcbond_it 0.838 r_symmetry_hbond_refined 0.545 r_nbtor_refined 0.318 r_nbd_refined 0.205 r_symmetry_vdw_refined 0.204 r_xyhbond_nbd_refined 0.166 r_nbd_other 0.142 r_nbtor_other 0.119 r_chiral_restr 0.112 r_mcbond_other 0.067 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2352 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing