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THE MOLECULAR MECHANISM OF SUBSTRATE RECOGNITION AND CATALYSIS OF THE MEMBRANE ACYLTRANSFERASE PatA -- Complex of PatA with palmitate, mannose, and palmitoyl-6-mannose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5F2T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 The crystal of PatA was obtained by mixing 0.25ul of the protein (5 mg ml-1) in 5 mM D-(+)-mannose and 20 mM Tris-HCl buffer pH 7.5 with 0.25ul of a mother liquor containing, 100 mM Tris-HCl pH 7.0, 225 mM MgCl2 and 16% (w/v) PEG 8,000.
Crystal Properties Matthews coefficient Solvent content 2.03 39.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.69 α = 90 b = 83.86 β = 110.98 c = 98.43 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2015-05-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9686 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.41 28.77 97.17 0.1125 0.989 12.76 3.3 40218
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.41 2.5 90.55 0.4939 0.773 3.3
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5F2T 2.41 28.77 1.45 40218 2049 97.17 0.1887 0.1817 0.1841 0.2127 0.2091 Random 44.52
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 17.301 f_angle_d 0.561 f_chiral_restr 0.038 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7808 Nucleic Acid Atoms Solvent Atoms 145 Heterogen Atoms 117
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing