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Crystal structure of LpxK from Aquifex aeolicus at 1.9 angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4EHW PDB ENTRY 4EHW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 hanging drop, vapor diffusion 7.5 293 The reservoir solution contained 60% MPD and 0.1 M Hepes pH 7.5. The drop contained ~1 mg/ml protein, 54% MPD, 90 mM Hepes pH 7.5, 2 mM Hepes pH 8.0, 75 mM NaCl, 2% glycerol, ~0.03% DDM, 2 mM MgCl2, 0.4 mM AMP-PNP, 0.4 mM methyl-2-acetamido-2-deoxy-B-D-glucopyranoside. hanging drop, vapor diffusion, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.09 60.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.783 α = 90 b = 69.049 β = 90 c = 106.079 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 2011-06-12 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 1.9 50 99.8 0.059 9.4 5.6 36583 36493 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 1.9 1.93 97.5 0.563 4.7 1766
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 4EHW 1.9 23.021 0.11 36493 34603 1731 94.8 0.1737 0.1723 0.1869 0.1995 0.2142 RANDOM 44.4362
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] 3.7361 1.3072 -5.0433
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.355 f_angle_d 1.02 f_chiral_restr 0.07 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2582 Nucleic Acid Atoms Solvent Atoms 208 Heterogen Atoms 79
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