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Crystal Structure of Authentic Providence Virus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OHF PDB entry 1ohf
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 2 ul of 7mg/ml virus solution (20mM Tris pH 7.5) added to 2 ul of 100mM Tris pH 7.5, 0.5-1.5% PEG8000, 10-100mM NaCl. Plates about 0.1 mm in size appear in 1-4 weeks., vapor diffusion, hanging drop, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.5 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 659.79 α = 90 b = 434.07 β = 126.13 c = 415.85 γ = 90
Symmetry Space Group C 1 2 1
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 315 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 1.0 SSRL BL11-1
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 3.8 50 29.6 0.158 3.6 1.3 272211 -0.5
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 3.8 3.94 28.2 0.249 1.9 1.2 25858
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT not used PDB entry 1ohf 3.8 49.42 263822 263822 28.6 0.285 0.285 0.285 0.2609 not used 20.945
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] -5.452 -3.085 6.198 -0.746
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.2 c_scangle_it 2.068 c_angle_deg 1.7 c_mcangle_it 1.629 c_scbond_it 1.251 c_improper_angle_d 1.06 c_mcbond_it 0.959 c_bond_d 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16549 Nucleic Acid Atoms 77 Solvent Atoms 6 Heterogen Atoms 2
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement PDB_EXTRACT data extraction Blu-Ice data collection HKL-2000 data reduction HKL-2000 data scaling GLRF phasing