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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 2.13 42.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.531 α = 90 b = 80.896 β = 108.08 c = 63.209 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 IMAGE PLATE MAR scanner 345 mm plate Mirrors 2013-12-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.5418
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 1.67 60.09 97.1 0.143 10.8 5.7 62327 62327
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 1.68 1.77 92.3 0.313 2.3 1.8
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 (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 1.67 60.09 62327 59145 3158 96.26 0.1729 0.17034 0.17 0.22097 0.2198 RANDOM 14.355
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] -0.22 -0.07 0.49 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.12 r_dihedral_angle_3_deg 13.693 r_dihedral_angle_1_deg 7.361 r_dihedral_angle_4_deg 4.995 r_angle_refined_deg 2.038 r_chiral_restr 0.148 r_bond_refined_d 0.02 r_gen_planes_refined 0.012 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.12 r_dihedral_angle_3_deg 13.693 r_dihedral_angle_1_deg 7.361 r_dihedral_angle_4_deg 4.995 r_angle_refined_deg 2.038 r_chiral_restr 0.148 r_bond_refined_d 0.02 r_gen_planes_refined 0.012 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 4596 Nucleic Acid Atoms Solvent Atoms 628 Heterogen Atoms 131
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling