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Structure of the Aquifex aeolicus LpxC/LPC-069 complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DRO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.25 mg/mL compound,
4 mg/mL protein,
50 mM potassium chloride,
12.5 mM HEPES pH 7.0,
1 mM dithiothreitol,
25 microM zinc sulfate,
0.5% DMSO,
1.25 M diammonium hydrogen phosphate,
0.05 M Tris pH 7.7,
2.5% Glycerol
Crystal Properties Matthews coefficient Solvent content 2.65 53.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.99 α = 90 b = 65.99 β = 90 c = 132.42 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 100 CCD RAYONIX MX300-HS 2014-10-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1 APS 22-ID
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 1.62 29.531 99.99 20.13 12.4 41386
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 5DRO 1.62 29.531 1.4 41379 2009 99.99 0.1396 0.1388 0.1399 0.1537 0.1535
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 10.106 f_angle_d 0.899 f_chiral_restr 0.062 f_plane_restr 0.009 f_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2156 Nucleic Acid Atoms Solvent Atoms 441 Heterogen Atoms 59
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing