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Crystal structure of Aquifex aeolicus LpxC deacetylase complexed with palmitate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1P42 PDB entry 1P42
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 294 PEG 3350, NaCl, ZnSO4, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.99 58.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.61 α = 90 b = 101.61 β = 90 c = 124.18 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 IMAGE PLATE RIGAKU RAXIS IV 2004-08-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.7 50 0.115 0.115 10.4 5.83 19665 1 15.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.7 2.8 98.2 0.115 0.115 4.7 5.84 2012
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1P42 2.7 50 19524 19524 1919 97.4 0.2011 0.2011 0.201 0.239 RANDOM 27.7
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] -1.63 4.52 -1.63 3.26
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.3 c_scangle_it 2.86 c_mcangle_it 1.799 c_scbond_it 1.798 c_angle_deg 1.2 c_mcbond_it 1.078 c_improper_angle_d 0.76 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4296 Nucleic Acid Atoms Solvent Atoms 119 Heterogen Atoms 44
Software Software Software Name Purpose Crystal data collection d*TREK data reduction AMoRE phasing CNS refinement CrystalClear data reduction d*TREK data scaling