☰ Navigation Tabs
2.4 Angstrom Crystal Structure of Superantigen-like Protein from Staphylococcus aureus.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3URY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 295 Protein: 7.4mG/mL, 0.25M Sodium chloride, 0.01M Tris-HCl (pH 8.3);
Screen: PACT (D6), 0.1M MMT buffer (pH 9.0), 25% (w/v) PEG 1500., VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 1.88 34.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.64 α = 90 b = 106.504 β = 90 c = 162.085 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD MARMOSAIC 300 mm CCD Beryllium lenses 2011-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 2.4 30 99.9 0.078 21.8 6.6 31397 31397 -3 58.2
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 2.4 2.44 100 0.523 3.6 6.5 1519
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3URY 2.4 29.67 29519 29519 1569 99.87 0.19809 0.19809 0.19486 0.1973 0.25967 0.2609 RANDOM 51.916
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] -1.76 1.46 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.477 r_dihedral_angle_4_deg 11.54 r_dihedral_angle_3_deg 8.522 r_scangle_it 3.309 r_dihedral_angle_1_deg 2.363 r_scbond_it 2.112 r_mcangle_it 1.264 r_angle_refined_deg 1.219 r_angle_other_deg 0.708 r_mcbond_it 0.674
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.477 r_dihedral_angle_4_deg 11.54 r_dihedral_angle_3_deg 8.522 r_scangle_it 3.309 r_dihedral_angle_1_deg 2.363 r_scbond_it 2.112 r_mcangle_it 1.264 r_angle_refined_deg 1.219 r_angle_other_deg 0.708 r_mcbond_it 0.674 r_mcbond_other 0.162 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6357 Nucleic Acid Atoms Solvent Atoms 222 Heterogen Atoms 2
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling