☰ Navigation Tabs
N-Domain of human adhesion/growth-regulatory galectin-9
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 8.5 298 26 % (w/v) PEG 4000, 0.25 M Na acetate, 0.1 M Tris (pH 8.5), VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2 38.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.813 α = 90 b = 37.813 β = 90 c = 153.5 γ = 120
Symmetry Space Group P 31 1 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 210r M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM16 ESRF BM16
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 2.01 32.03 95.6 0.074 17.8 6.6 8444 2
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) 2.01 2.12 77.5 0.215 6.7 5.6
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 2.03 32.03 7678 370 95.5 0.194 0.191 0.2233 0.26 0.2839 RANDOM 33.94
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] -0.09 -0.04 -0.09 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.482 r_dihedral_angle_4_deg 22.315 r_dihedral_angle_3_deg 15.153 r_dihedral_angle_1_deg 12.487 r_scangle_it 4.224 r_scbond_it 2.951 r_angle_refined_deg 1.817 r_mcangle_it 1.709 r_mcbond_it 0.971 r_chiral_restr 0.127
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.482 r_dihedral_angle_4_deg 22.315 r_dihedral_angle_3_deg 15.153 r_dihedral_angle_1_deg 12.487 r_scangle_it 4.224 r_scbond_it 2.951 r_angle_refined_deg 1.817 r_mcangle_it 1.709 r_mcbond_it 0.971 r_chiral_restr 0.127 r_bond_refined_d 0.02 r_gen_planes_refined 0.014 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 1119 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling