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Crystal Structure of the Lectin Domain From the F17-like Adhesin, UclD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Se-SAD model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 16% PEG 4000, 0.1M Tris HCl pH 8.5, 0.2M MgCl2
Crystal Properties Matthews coefficient Solvent content 2.08 40.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.089 α = 90 b = 91.871 β = 96.46 c = 64.932 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 ADSC QUANTUM 315r 2010-01-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.008 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.05 91.87 88.8 0.079 0.034 11.9 5 144393 5.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.05 1.11 43.8 0.336 0.308 2.1 2
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 Se-SAD model 1.05 91.87 137073 7242 88.7 0.11839 0.11711 0.1177 0.14252 0.1427 RANDOM 11.786
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 -0.08 -0.15 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.311 r_sphericity_free 28.643 r_dihedral_angle_4_deg 23.326 r_sphericity_bonded 10.845 r_dihedral_angle_3_deg 10.302 r_dihedral_angle_1_deg 7.467 r_rigid_bond_restr 7.128 r_long_range_B_refined 5.417 r_scangle_other 4.791 r_long_range_B_other 4.721
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.311 r_sphericity_free 28.643 r_dihedral_angle_4_deg 23.326 r_sphericity_bonded 10.845 r_dihedral_angle_3_deg 10.302 r_dihedral_angle_1_deg 7.467 r_rigid_bond_restr 7.128 r_long_range_B_refined 5.417 r_scangle_other 4.791 r_long_range_B_other 4.721 r_scbond_it 3.914 r_scbond_other 3.913 r_mcangle_other 2.268 r_mcangle_it 2.266 r_angle_refined_deg 2.232 r_mcbond_it 1.917 r_mcbond_other 1.913 r_angle_other_deg 1.417 r_chiral_restr 0.148 r_bond_refined_d 0.027 r_gen_planes_refined 0.012 r_gen_planes_other 0.008 r_bond_other_d 0.003 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2914 Nucleic Acid Atoms Solvent Atoms 646 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling SHELXD phasing