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Crystal structure of beta toxin from Staphylococcus aureus F277A, P278A mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Native Beta Toxin
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 PEG 4000, 0.1 M MES, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 1.92 35.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.176 α = 90 b = 68.668 β = 90 c = 127.842 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 ADSC QUANTUM 315 mirrors 2008-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.90020 APS 14-BM-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.75 26.18 93.5 56896 54177
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 (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 Native Beta Toxin 1.75 26.18 54177 51436 2741 95.35 0.204 0.201 0.1995 0.26 0.2575 RANDOM 26.598
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 r_dihedral_angle_2_deg 36.756 r_dihedral_angle_3_deg 15.783 r_dihedral_angle_4_deg 11.047 r_dihedral_angle_1_deg 6.863 r_scangle_it 3.373 r_scbond_it 2.419 r_mcangle_it 1.805 r_angle_refined_deg 1.563 r_mcbond_it 1.109 r_symmetry_vdw_refined 0.403
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.756 r_dihedral_angle_3_deg 15.783 r_dihedral_angle_4_deg 11.047 r_dihedral_angle_1_deg 6.863 r_scangle_it 3.373 r_scbond_it 2.419 r_mcangle_it 1.805 r_angle_refined_deg 1.563 r_mcbond_it 1.109 r_symmetry_vdw_refined 0.403 r_nbtor_refined 0.309 r_nbd_refined 0.248 r_symmetry_hbond_refined 0.244 r_xyhbond_nbd_refined 0.183 r_chiral_restr 0.132 r_bond_refined_d 0.015 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4656 Nucleic Acid Atoms Solvent Atoms 536 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection HKL-3000 data reduction AMoRE phasing