☰ Navigation Tabs
Crystal structure of Ad37 fiber knob in complex with trivalent sialic acid inhibitor ME0408
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other unliganded Ad37 trimer
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.1 293 28% PEG 8000, 0.1M HEPES, 0.05M zinc acetate, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.41 48.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.93 α = 90 b = 69.28 β = 94.92 c = 74.56 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 PIXEL DECTRIS PILATUS 2M-F 2012-09-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA SLS X06DA
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 1.5 50 99.4 0.043 15.1 3.66 97896 97896 -3 -3 27.3
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) 1 1.5 1.54 96 0.72 1.7 3.5 6984
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 unliganded Ad37 trimer 1.5 45.66 97896 97895 1469 99.39 0.12861 0.12804 0.1399 0.16715 0.1738 RANDOM 25.349
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] -0.04 0.25 0.12 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.325 r_sphericity_free 22.739 r_dihedral_angle_3_deg 11.513 r_dihedral_angle_4_deg 9.355 r_sphericity_bonded 7.04 r_dihedral_angle_1_deg 6.844 r_angle_other_deg 3.411 r_rigid_bond_restr 3.024 r_angle_refined_deg 1.461 r_chiral_restr 0.081
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.325 r_sphericity_free 22.739 r_dihedral_angle_3_deg 11.513 r_dihedral_angle_4_deg 9.355 r_sphericity_bonded 7.04 r_dihedral_angle_1_deg 6.844 r_angle_other_deg 3.411 r_rigid_bond_restr 3.024 r_angle_refined_deg 1.461 r_chiral_restr 0.081 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4320 Nucleic Acid Atoms Solvent Atoms 643 Heterogen Atoms 128
Software Software Software Name Purpose RemDAq data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling