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Jacalin-carbohydrate interactions. Distortion of the ligand as a determinant of affinity.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KU8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 298 15% PEG 8000, 0.1M HEPES, pH 7.4, 10% (v/v) isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.12 42.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.53 α = 90 b = 80.88 β = 107.88 c = 63.04 γ = 90
Symmetry Space Group P 1 21 1
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 MARMOSAIC 225 mm CCD Bent collimating mirror and toroid 2013-10-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.98 ESRF BM14
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 1.7 60 98.2 0.077 11.5 5.4 60267 60267
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 1.7 1.79 97.1 0.761 2.1 5.4 8682
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1KU8 1.7 30.63 60267 57187 3053 97.97 0.1683 0.1683 0.16601 0.1655 0.21126 0.2104 RANDOM 26.714
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] -0.87 0.28 1.82 -0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.394 r_dihedral_angle_3_deg 11.369 r_dihedral_angle_1_deg 6.397 r_dihedral_angle_4_deg 4.256 r_angle_refined_deg 1.475 r_chiral_restr 0.106 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.394 r_dihedral_angle_3_deg 11.369 r_dihedral_angle_1_deg 6.397 r_dihedral_angle_4_deg 4.256 r_angle_refined_deg 1.475 r_chiral_restr 0.106 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4552 Nucleic Acid Atoms Solvent Atoms 475 Heterogen Atoms 44
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling