☰ Navigation Tabs
Crystallographic structure of a cubic form of STMV grown from nitrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OQ8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 279 Crystals were grown by sitting drop vapor diffusion in Cryschem plates using 0.6 ml reservoirs. Drops were equal amounts of a 5 mg/ml virus stock solution buffered with 0.1 M phosphate at pH 6.5, and the reservoir solution which was 20% w/v sodium nitrate in 0.1 M phosphate at pH 6.0. Crystallization was carried out at 4 degrees C.
Crystal Properties Matthews coefficient Solvent content 3.05 59.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 234.05 α = 90 b = 234.05 β = 90 c = 234.05 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 173 CCD MAR CCD 165 mm 2002-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.0 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 3.18 105 0.65 0.143 0.142 0.964 11.5 3.8 45796 50.45
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.18 3.25 0.235 0.46 2.2
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 4OQ8 3.19 75 1.33 45793 1923 64.22 0.2627 0.2608 0.2372 0.2732 0.2611 54.84
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 10.1231 f_angle_d 0.4849 f_chiral_restr 0.0467 f_plane_restr 0.0044 f_bond_d 0.0026
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 22980 Nucleic Acid Atoms Solvent Atoms 1583 Heterogen Atoms 417
Software Software Software Name Purpose PHENIX refinement d*TREK data reduction d*TREK data scaling PHASER phasing