☰ Navigation Tabs
Crystal structure of Ad37 fiber knob in complex with trivalent sialic acid inhibitor ME0407
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 7.2 293 25% PEG 8000, 0.1M HEPES, 0.05M zinc acetate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.44 49.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.32 α = 90 b = 69.68 β = 94.43 c = 74.78 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 50 100 0.046 14.6 3.7 99467 99467 -3 -3 27.5
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 95.7 0.917 1.3 3.5 7042
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 45.96 99467 99466 1492 99.46 0.13452 0.13376 0.1449 0.18464 0.1873 RANDOM 24.715
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] 0.47 0.63 -0.37 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.265 r_sphericity_free 25.645 r_dihedral_angle_4_deg 21.994 r_dihedral_angle_3_deg 11.949 r_sphericity_bonded 7.385 r_dihedral_angle_1_deg 6.7 r_angle_other_deg 3.425 r_rigid_bond_restr 2.673 r_angle_refined_deg 1.409 r_chiral_restr 0.079
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.265 r_sphericity_free 25.645 r_dihedral_angle_4_deg 21.994 r_dihedral_angle_3_deg 11.949 r_sphericity_bonded 7.385 r_dihedral_angle_1_deg 6.7 r_angle_other_deg 3.425 r_rigid_bond_restr 2.673 r_angle_refined_deg 1.409 r_chiral_restr 0.079 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_gen_planes_other 0.003 r_bond_other_d 0.002 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 621 Heterogen Atoms 117
Software Software Software Name Purpose RemDAq data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling