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Crystal structure of octameric pore form of gamma-hemolysin from Staphylococcus aureus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LKF PDB ENTRIES 1LKF, 2QK7 and 3ANZ experimental model PDB 2QK7 PDB ENTRIES 1LKF, 2QK7 and 3ANZ experimental model PDB 3ANZ PDB ENTRIES 1LKF, 2QK7 and 3ANZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 293 Sodium acetate, ammonium acetate, MPD, pH 4.6, vapor diffusion, sitting drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.7 66.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 206.454 α = 90 b = 206.141 β = 90 c = 190.299 γ = 90
Symmetry Space Group C 2 2 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 RAYONIX MX225HE 2010-07-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.00000 SPring-8 BL41XU
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 2.49 43.298 98.9 0.111 14.32 138838 -3 39.415
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.49 2.65 96.3 0.651 0.703 3.47
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (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 PDB ENTRIES 1LKF, 2QK7 and 3ANZ 2.495 43.298 138828 3992 98.91 0.2068 0.2041 0.2364 0.232 RANDOM (LATTICE SYMMETRY CONSIDERED) 43.5237
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] -13.5408 -17.2704 30.8111
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.543 f_angle_d 1.125 f_chiral_restr 0.061 f_bond_d 0.009 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17896 Nucleic Acid Atoms Solvent Atoms 449 Heterogen Atoms 32
Software Software Software Name Purpose XSCALE data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction BSS data collection XDS data reduction XDS data scaling