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The Atomic Structure of Adeno-Associated Virus (AAV-2), a Vector for Human Gene Therapy
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DPV PDB entries 4dpv, 1dnv experimental model PDB 1DNV PDB entries 4dpv, 1dnv
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.3 295 PEG 6000, magnesium chloride, hepes, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 249.69 α = 90 b = 249.69 β = 101.16 c = 644.76 γ = 120
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 4 1998-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 0.92 CHESS F1
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 3 39.8 56 0.156 6.3 2 1462541 -3 -3 38.676
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 3.43 3.56 43 0.309 5.9 2 25132
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) 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 Selection Details Mean Isotropic B X-RAY DIFFRACTION Molecular replacement at 15A, then phase extension by symmetry averaging PDB entries 4dpv, 1dnv 3 39.8 1462541 7117 56 0.339 0.338 0.338 0.3284 0.342 Random 23.5
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] 4.076 -6.626 -3.166 -8.503
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26.68 c_angle_deg 2.2 c_improper_angle_d 1.68 c_bond_d 0.02
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4152 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose GLRF phasing RAVE model building CCP4 model building CNS refinement DENZO data reduction SCALEPACK data scaling RAVE phasing CCP4 phasing