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Crystal structure of E.coli BamA beta-barrel in complex with darobactin (crystal form 1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6QGW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.06 M Magnesium chloride/Calcium Chloride, 0.1 M imidazole/2-(N-morpholino)ethanesulfonic acid pH 6.5, 12.5% v/v 2-Methyl-2,4-pentanediol, 12.5% w/v Polyethylene glycol 1,000, and 12.5% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.75 55.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.995 α = 90 b = 82.563 β = 108.64 c = 94.305 γ = 90
Symmetry Space Group I 1 2 1
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 EIGER X 16M 2019-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.000009 SLS X06SA
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 2.3 46.602 99.7 0.156 0.172 0.072 0.997 7.1 11.7 22630
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 2.3 2.38 98.8 1.456 1.602 0.66 0.535 1.3 8.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 FREE R-VALUE 6QGW 2.3 46.602 1.35 22630 1129 99.74 0.2059 0.2045 0.2046 0.2315 0.2329 49.6919
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2916 Nucleic Acid Atoms Solvent Atoms 201 Heterogen Atoms 258
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing