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Crystal Structure of Human Adenovirus 52 Short Fiber Knob in Complex with 2-O-Methyl-5-N-Acetylneuraminic Acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NOB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 15% (w/V) PEG1000, 12.5% (w/V) PEG3350, 12.5% (w/V) MPD, 0.02 mM of each Na L glutamate, DL alanine, glycine, DL lysine HCl, and DL serine, 0.1 M Tris/Bicine
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.77 α = 90 b = 81.61 β = 90 c = 92.65 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 2013-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.00 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 1.65 50 99.7 0.109 0.999 25.4 13.1 58970
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.75 98.3 1.303 0.683 2 12.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 1nob 1.65 37.48 1.35 58963 2946 99.72 0.1522 0.151 0.1524 0.1737 0.1746 18.95
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 12.744 f_angle_d 1.39 f_chiral_restr 0.101 f_bond_d 0.011 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3786 Nucleic Acid Atoms Solvent Atoms 351 Heterogen Atoms 93
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing