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Structure of the membrane integral lipoprotein N-acyltransferase Lnt C387A mutant from E. coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5N6H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 293 8 % (v/v) MPD
0.1 M MES pH 6
0.4 M ammonium citrate
0.1 M sodium malonate pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.29 62.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.22 α = 90 b = 142.95 β = 90 c = 197.71 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 PIXEL DECTRIS PILATUS 6M-F 2016-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.99998 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.9 49.79 97.9 7.72 5.4 34916
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 5N6H 2.9 49.79 1.33 34807 1699 97.66 0.2288 0.2271 0.2378 0.2633 0.2625
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 14.424 f_angle_d 0.798 f_chiral_restr 0.05 f_plane_restr 0.006 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7845 Nucleic Acid Atoms Solvent Atoms 13 Heterogen Atoms 513
Software Software Software Name Purpose XDS data reduction XSCALE data scaling MOLREP phasing BUSTER refinement PHENIX refinement Coot model building