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Crystal structure of LpxK from Aquifex aeolicus in complex with ADP/Mg2+ at 2.2 angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4EHX PDB ENTRY 4EHX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 sitting drop, vapor diffusion 7.5 293 The reservoir solution contained 60% MPD and 0.1 M Hepes pH 7.5. The drop contained 20% seed stock, ~1 mg/ml protein, 48% MPD, 80 mM Hepes pH 7.5, 4 mM Hepes pH 8.0, 130 mM NaCl, 3.4% glycerol, ~0.06% DDM, 1.8 mM ATP, 1.8 mM MgCl2, sutting drop, vapor diffusion, temperature 293K, sitting drop, vapor diffusion
Crystal Properties Matthews coefficient Solvent content 3.5 64.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.11 α = 90 b = 75.61 β = 90 c = 104.2 γ = 90
Symmetry Space Group P 21 21 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 MARMOSAIC 225 mm CCD 2011-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.00 APS 22-BM
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 2.199 50 98 0.049 13.6 4.7 26821 26285 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.199 2.24 86.9 0.434 3.6 1151
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 PDB ENTRY 4EHX 2.199 28.401 0.08 26285 24602 1999 91.73 0.1808 0.1779 0.1992 0.2132 0.2375 65.3908
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] -0.2843 11.4845 -11.2002
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.299 f_angle_d 1.157 f_chiral_restr 0.073 f_bond_d 0.008 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2520 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 47
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction SERGUI data collection HKL-2000 data reduction HKL-2000 data scaling