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The structure of the neurotropic AAVrh.8 viral vector
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QA0 AAV8 VP1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 298 Crystallization drops consisted of virus sample (10 mg/ml) in 1X PBS mixed with reservoir solution (5.5% PEG8000 in 1xPBS) at a 1:1 ratio (v/v) and equilibrated against 1 ml of reservoir solution at 298K. pH 7.4; temperature 298K; hanging-drop vapor-diffusion, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.42 49.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 355.5 α = 90 b = 358.9 β = 90 c = 371.5 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 CCD ADSC QUANTUM 270 mirrors 2010-06-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 0.91860 CHESS F1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 3.5 50 90 0.176 3.2 2.8 532197 487416
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.5 3.63 86 0.371 2.1 50545
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 AAV8 VP1 3.5 50 532197 487416 24216 0.217 0.217 0.217 0.2268 0.219 0.2288 random
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 c_angle_deg 1.37 c_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4124 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms 24
Software Software Software Name Purpose HKL-2000 data collection PHENIX model building CNS refinement HKL-2000 data reduction SCALEPACK data scaling PHENIX phasing