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Crystal Structure of Human Adenovirus 52 Short Fiber Knob Mutant K349R in Complex with alpha-(2,8)-Pentasialic Acid (DP5)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6G47
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293.15 12.5 % (v/v) MPD; 12.5 % (w/v) PEG3350; 25 % (w/v) PEG1000; 0.1 M Tris/Bicine pH 8.5; 1.6 mM of each Glycine, Na L-Glutamate, DL-Alanine, DL-Lysine, DL-Serine; Seed stock N243R 1:100
Crystal Properties Matthews coefficient Solvent content 1.82 32.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.501 α = 90 b = 82.245 β = 90 c = 93.458 γ = 90
Symmetry Space Group P 21 21 21
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 2020-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.999997 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) CC (Half) 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 2.1 46.73 99.8 0.291 0.985 5.98 5.16 29147 24.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.22 99.9 1.337 0.497 1.35
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.1 46.73 1.36 29145 1458 99.83 0.1994 0.1984 0.1989 0.219 0.2182 24.79
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 20.1603 f_angle_d 1.9018 f_chiral_restr 0.1426 f_bond_d 0.0138 f_plane_restr 0.0125
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3825 Nucleic Acid Atoms Solvent Atoms 224 Heterogen Atoms 113
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction XDS data scaling PHASER phasing