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Crystal Structures of EAP Domains from Staphylococcus aureus Reveal an Unexpected Homology to Bacterial Superantigens
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YN5 EapH1, pdb entry 1YN5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.4 293 PEG 8000, ammonium sulfate, MES, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.59 52.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.116 α = 90 b = 64.116 β = 90 c = 141.706 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 CCD ADSC QUANTUM 4 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A 0.9793 NSLS X4A
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 1.35 30 88.8 40720 13.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.35 1.45 70.3
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 EapH1, pdb entry 1YN5 1.35 29.87 40720 2031 85.1 0.218 0.218 0.217 0.23 0.2299 RANDOM 16.4
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] 0.18 0.55 0.18 -0.36
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.1 c_scangle_it 2.92 c_mcangle_it 2.09 c_scbond_it 2.01 c_angle_deg 2 c_improper_angle_d 1.3 c_mcbond_it 1.29 c_bond_d 0.02 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.1 c_scangle_it 2.92 c_mcangle_it 2.09 c_scbond_it 2.01 c_angle_deg 2 c_improper_angle_d 1.3 c_mcbond_it 1.29 c_bond_d 0.02 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1520 Nucleic Acid Atoms Solvent Atoms 304 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing CNS refinement