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2.9 Angstrom Crystal Structure of Putative Exotoxin 3 from Staphylococcus aureus.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2RDH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 295 Protein: 8.0 mg/ml, 0.5 M Sodium chloride, 0.01 M Tris-HCL buffer pH(8.3); Screen: PEGs (C10), 0.1M MES (pH 6.5), 25% (w/v) PEG 8000., VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.09 41.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.427 α = 90 b = 90.623 β = 90 c = 159.711 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 100 CCD MARMOSAIC 300 mm CCD Beryllium lenses 2014-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.9 30 95.4 0.121 0.121 10.4 4.2 13668 13668 -3 58.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 2.95 100 0.5 0.5 2.7 4.3 714
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 2RDH 2.9 29.96 12253 12253 1372 95.01 0.23143 0.23143 0.22562 0.2234 0.28252 0.2792 RANDOM 54.042
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] -3.76 -1.67 5.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.031 r_dihedral_angle_4_deg 12.522 r_dihedral_angle_3_deg 11.672 r_long_range_B_refined 6.897 r_long_range_B_other 6.875 r_mcangle_it 4.152 r_mcangle_other 4.152 r_scangle_other 4.123 r_mcbond_it 2.52 r_mcbond_other 2.519
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.031 r_dihedral_angle_4_deg 12.522 r_dihedral_angle_3_deg 11.672 r_long_range_B_refined 6.897 r_long_range_B_other 6.875 r_mcangle_it 4.152 r_mcangle_other 4.152 r_scangle_other 4.123 r_mcbond_it 2.52 r_mcbond_other 2.519 r_scbond_it 2.445 r_scbond_other 2.418 r_dihedral_angle_1_deg 2.078 r_angle_refined_deg 1.538 r_angle_other_deg 1.03 r_chiral_restr 0.09 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.004 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4588 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms 3
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling