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Crystal structure of beta toxin from Staphylococcus aureus F277A, P278A mutant with bound calcium ions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Wild-type beta toxin from Staphylococcus aureus
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 100 mM MES, 28% PEG 4000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.15 42.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.093 α = 90 b = 70.195 β = 90 c = 129.584 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 125 IMAGE PLATE RIGAKU RAXIS IV mirrors 2008-09-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54178
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 2.6 35 98.9 0.057 31.8 5.7 19618 19618
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 2.6 2.64 99.8 0.357 4.5 5.6 967
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 Wild-type beta toxin from Staphylococcus aureus 2.6 34.04 19555 1000 98.69 0.223 0.221 0.2196 0.275 0.2745 RANDOM 58.135
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] 1.11 -0.16 -0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.246 r_dihedral_angle_3_deg 14.3 r_dihedral_angle_4_deg 11.142 r_dihedral_angle_1_deg 4.488 r_scangle_it 2.506 r_scbond_it 1.857 r_angle_refined_deg 1.385 r_mcangle_it 1.285 r_mcbond_it 0.935 r_nbtor_refined 0.321
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.246 r_dihedral_angle_3_deg 14.3 r_dihedral_angle_4_deg 11.142 r_dihedral_angle_1_deg 4.488 r_scangle_it 2.506 r_scbond_it 1.857 r_angle_refined_deg 1.385 r_mcangle_it 1.285 r_mcbond_it 0.935 r_nbtor_refined 0.321 r_nbd_refined 0.209 r_symmetry_vdw_refined 0.19 r_xyhbond_nbd_refined 0.165 r_chiral_restr 0.098 r_symmetry_hbond_refined 0.025 r_metal_ion_refined 0.02 r_bond_refined_d 0.011 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4644 Nucleic Acid Atoms Solvent Atoms 35 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing