☰ Navigation Tabs
Structure of the C-terminal SpoA domain of Shigella flexneri Spa33
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YAB 1YAB, 1O9Y experimental model PDB 1O9Y 1YAB, 1O9Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 294 10% (v/v) isopropanol, 0.1 M Na HEPES pH7.0, 10% (w/v) PEG 4000
Crystal Properties Matthews coefficient Solvent content 1.89 35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.3 α = 90 b = 27.82 β = 90.03 c = 104.44 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 CCD ADSC QUANTUM 315 2011-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 2.3 51.3 99.5 0.042 21.3 3.6 13523
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 2.3 2.38 99.1 0.77 2.1 3.6
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1YAB, 1O9Y 2.3 51.3 1.34 13522 1369 99.42 0.1768 0.1739 0.1751 0.2099 0.1819 Phenix selected for twin refinement
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 15.14 f_angle_d 1.03 f_chiral_restr 0.071 f_bond_d 0.007 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2273 Nucleic Acid Atoms Solvent Atoms 65 Heterogen Atoms 16
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling Aimless data scaling PHASER phasing