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Crystallographic structure of a cubic crystal form of STMV grown from bromide
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 6 to 8 ul and composed of equal volumes of a 5 mg/ml virus stock solution buffered at pH 6.5 with 0.1M phosphate, and the reservoir solution. The reservoir solution was 18% w/v NaBr buffered with 0.1 M phosphate at pH 6.0. Crystallization was carried out at 4 degrees C.
Crystal Properties Matthews coefficient Solvent content 3.07 59.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 234.65 α = 90 b = 234.65 β = 90 c = 234.65 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 2002-06-21 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 3.5 105 73 0.21 0.2 0.94 7.7 4.6 38017 50.24
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.5 3.65 0.32 0.3 0.32 1.1
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 3.8 56.91 1.33 33573 1305 78.77 0.2188 0.2131 0.1952 0.2853 0.2857 85.34
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 10.6411 f_angle_d 0.649 f_chiral_restr 0.0485 f_plane_restr 0.0069 f_bond_d 0.0053
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 23322 Nucleic Acid Atoms Solvent Atoms 580 Heterogen Atoms 200
Software Software Software Name Purpose PHENIX refinement d*TREK data reduction d*TREK data scaling PHASER phasing