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Crystal structure of E. coli LpoA amino terminal domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4P29
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 Drops contained 0.5 ul protein and 0.5 ul precipitant and equilibrated against precipitant by vapor diffusion.
Protein: 19 mg/ml in 50 mM NaCl, 1 mM dithiothreitol, 50 mM TrisHCl pH 7.5.
Precipitant contained: 0.03 M magnesium chloride
hexahydrate, 0.03 M calcium chloride dihydrate, 5% glycerol, 0.1 M Buffer System 1, pH 6.5, 10% PEG 20,000, 17% PEG 550 MME
Buffer System 1: 30 mL MES (pH 3.11) was titrated with 24.1 mL Imidazole (pH 10.23) to a final pH of 6.5
Crystal Properties Matthews coefficient Solvent content 2.38 48.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.001 α = 90 b = 70.001 β = 90 c = 97.802 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 140 PIXEL DECTRIS EIGER X 9M mirrors 2017-08-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.97717 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.1 30 99.8 0.104 0.109 0.032 6.7 10.9 14791 27.23
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.18 99.6 0.76 0.837 0.339 0.692 5.7
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4P29 2.101 22.697 1.47 14660 1465 99.34 0.1808 0.1771 0.2132 0.1964 42.4992
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 11.044 f_angle_d 0.441 f_chiral_restr 0.033 f_bond_d 0.002 f_plane_restr 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1769 Nucleic Acid Atoms Solvent Atoms 151 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction HKL-2000 data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction