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The Structure of Tomato Aspermy Virus by X-Ray Crystallography
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F15 PDB ENTRY 1F15
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 14-17% Ethanol, 100mM tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.36 63.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 294.296 α = 90 b = 327.393 β = 90 c = 382.066 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 IMAGE PLATE MARRESEARCH 1997-04-01 M SINGLE WAVELENGTH 2 1 x-ray 298 IMAGE PLATE MARRESEARCH 1997-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X12B 1.15000 NSLS X12B 2 SYNCHROTRON SSRL BEAMLINE BL7-1 1.08000 SSRL BL7-1
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 1,2 3.4 49.72 62.4 0.23 7.9 1.522 156531 156468
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 3.4 3.46 2.2 269
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 1F15 3.4 50 2 156468 127436 6391 50.8 0.278 0.218 0.2134 0.228 0.225 RANDOM 105
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 x_dihedral_angle_d 29.3 x_scangle_it 22.85 x_scbond_it 16.25 x_mcangle_it 12.25 x_mcbond_it 7.5 x_angle_deg 1.66 x_improper_angle_d 1.03 x_bond_d 0.009 x_bond_d_na x_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 29.3 x_scangle_it 22.85 x_scbond_it 16.25 x_mcangle_it 12.25 x_mcbond_it 7.5 x_angle_deg 1.66 x_improper_angle_d 1.03 x_bond_d 0.009 x_bond_d_na x_bond_d_prot x_angle_d x_angle_d_na x_angle_d_prot x_angle_deg_na x_angle_deg_prot x_dihedral_angle_d_na x_dihedral_angle_d_prot x_improper_angle_d_na x_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4239 Nucleic Acid Atoms 63 Solvent Atoms Heterogen Atoms 6
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling X-PLOR model building X-PLOR refinement X-PLOR phasing