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Alpha-Hemolysin of S.aureus (monomer) in complex with the small molecule N-(3-(Diethylamino)propyl)-1-(6-(p-tolyl)imidazo[2,1-b][1,3,4]thiadiazol-2-yl)piperidine-4-carboxamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4YHD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 2 M Ammonium sulfate
18.3% (v/v) Glycerol
0.1 M Lithium sulfate
2.5 mg/ml protein + 0.250 mM LDC205092 (5% (v/v) DMSO)
Crystal Properties Matthews coefficient Solvent content 3.01 59.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.765 α = 90 b = 95.765 β = 90 c = 157.65 γ = 120
Symmetry Space Group P 62 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2016-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.033 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.08 82.93 100 0.501 0.507 0.075 0.984 14.5 48.6 26347
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.08 2.19 100 1.539 1.574 0.331 0.433 22.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.08 57.14 1.34 26287 1272 99.97 0.2413 0.2394 0.2396 0.2793 0.2798
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 f_dihedral_angle_d 6.916 f_angle_d 0.479 f_chiral_restr 0.044 f_plane_restr 0.005 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2331 Nucleic Acid Atoms Solvent Atoms 203 Heterogen Atoms 96
Software Software Software Name Purpose autoPROC data processing XDS data reduction Aimless data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction