☰ Navigation Tabs
Structure of Turnip Yellow Mosaic Virus at 100 K
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AUY PDB ENTRY 1AUY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.4 298 1.0-1.7 M NH4PO4, 0.1 M MES buffer, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 4.15 70.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 511.53 α = 90 b = 511.53 β = 90 c = 303.76 γ = 120
Symmetry Space Group P 64 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 100 CCD ADSC QUANTUM 4 Vertical and toroidal focusing mirror 1998-12-11 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 4 Vertical and toroidal focusing mirror 1999-11-20 M SINGLE WAVELENGTH 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0 ALS 5.0.2 2 SYNCHROTRON ALS BEAMLINE 5.0.2 1.25 ALS 5.0.2
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 1,2 2.61 59.12 35.3 0.106 7.49 3.2 247650 225845 34
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1,2 2.61 2.65 0.5 -0.41 1 172
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-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 THROUGHOUT PDB ENTRY 1AUY 2.9 59.12 2 246412 215839 10857 42.8 0.327 0.277 0.276 0.2658 0.289 0.2787 RANDOM 29.3
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] -5.62 6.21 -5.62 11.24
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 29.9 c_scangle_it 9.71 c_scbond_it 6.88 c_mcangle_it 6.35 c_mcbond_it 4.08 c_angle_deg 1.8 c_improper_angle_d 0.95 c_bond_d 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4065 Nucleic Acid Atoms 57 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling CNS phasing