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Structure of the globular C-terminal domain of P. aeruginosa LpoP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5XW7 homology model based on 5XW7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 294.15 (30 mg/mL purified protein in 20 mM HEPES, pH 8.0, 150 mM NaCl) and 1 uL of mother liquor (0.1 M HEPES pH 7.5, 2.5 M ammonium sulfate, 1% PEG 400, 2.5% 1,2-butanediol)
Crystal Properties Matthews coefficient Solvent content 2.1 41.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.757 α = 90 b = 154.584 β = 90.15 c = 54.083 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 2018-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.2 48.76 98.7 0.057 0.069 0.037 0.998 12.7 3.2 39974 33.68
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 2.2 2.27 98.6 0.378 0.453 0.247 0.864 3.2
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 homology model based on 5XW7 2.2 48.757 1.34 39858 1414 98.41 0.1955 0.1942 0.2298 0.2285 41.759
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 22.697 f_angle_d 0.987 f_chiral_restr 0.047 f_plane_restr 0.011 f_bond_d 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6194 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms 85
Software Software Software Name Purpose Aimless data scaling PHENIX refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing