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Lipid A secondary acyltransferase LpxM from Acinetobacter baumannii with catalytic residue substitution (E127A)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5KN7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 200 mM KBr
2.2 M (NH4)2SO4
Crystal Properties Matthews coefficient Solvent content 2.56 51.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.3 α = 90 b = 145.47 β = 90 c = 87.61 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 CCD ADSC QUANTUM 315r 2016-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0000 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.9 72.74 100 0.998 7.95 1.9 30262
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 5KN7 1.9 72.735 1.33 30262 871 99.9 0.2265 0.2252 0.2303 0.2712 0.2758 32.284
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 17.599 f_angle_d 1.1 f_chiral_restr 0.061 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2566 Nucleic Acid Atoms Solvent Atoms 105 Heterogen Atoms 121
Software Software Software Name Purpose Aimless data scaling PHENIX refinement PDB_EXTRACT data extraction iMOSFLM data reduction PHASER phasing