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Crystal structure of beta toxin from Staphylococcus aureus F277A, P278A mutant with bound magnesium ions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3I41 PDB entry 3I41
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 PEG 4000, 0.1 M MES, 5mM MgCl2, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 1.89 34.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.9 α = 90 b = 68.577 β = 90 c = 126.559 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 2007-10-11 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) 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 1.8 50 99.8 0.055 11.7 4.3 51464 51464
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) 1.8 1.83 99.5 0.472 2.6 3.8 2493
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3I41 1.8 28.16 51405 48742 2625 99.84 0.185 0.184 0.22 0.2087 RANDOM 28.979
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] 0.06 -0.13 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.67 r_dihedral_angle_3_deg 15.135 r_dihedral_angle_4_deg 9.516 r_dihedral_angle_1_deg 6.914 r_scangle_it 3.532 r_scbond_it 2.367 r_mcangle_it 1.87 r_angle_refined_deg 1.471 r_mcbond_it 1.116 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.67 r_dihedral_angle_3_deg 15.135 r_dihedral_angle_4_deg 9.516 r_dihedral_angle_1_deg 6.914 r_scangle_it 3.532 r_scbond_it 2.367 r_mcangle_it 1.87 r_angle_refined_deg 1.471 r_mcbond_it 1.116 r_nbtor_refined 0.313 r_symmetry_vdw_refined 0.279 r_nbd_refined 0.213 r_symmetry_hbond_refined 0.187 r_xyhbond_nbd_refined 0.145 r_chiral_restr 0.129 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4666 Nucleic Acid Atoms Solvent Atoms 472 Heterogen Atoms 12
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection CrystalClear data reduction AMoRE phasing