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Structural Studies of Bacteriophage alpha3 Assembly, X-Ray Crystallography
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Phix174 virion
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 318.15 3-5% PEG8000, 100 mM sodium citrate pH 5.0, 1 mM EDTA, 300 mM NaCl, 0.1 mM-mercapto-ethanol, and 0.02 % sodium azide, VAPOR DIFFUSION, SITTING DROP, temperature 318.15K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 290.258 α = 90 b = 332.115 β = 94.08 c = 337.698 γ = 90
Symmetry Space Group P 1 21 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 IMAGE PLATE MARRESEARCH 1998-09-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 1.0 APS 14-BM-C
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 3.5 100 75.3 0.08 20 4 597062 4 2 12.7
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 3.5 3.63 54.6 0.115 18 2.6 43298
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT Phix174 virion 3.5 82.45 597050 597050 59662 74.6 0.232 0.2376 0.234 0.2396 RANDOM
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] 0.7 26.04 -5.06 4.36
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.9 c_angle_deg 1.6 c_improper_angle_d 1.25 c_bond_d 0.017 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.9 c_angle_deg 1.6 c_improper_angle_d 1.25 c_bond_d 0.017 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4983 Nucleic Acid Atoms 110 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose JBluIce-EPICS data collection SnB phasing ENVELOPE model building CNS refinement ENVELOPE phasing