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The Transcriptional Regulator PrfA-A218G mutant from Listeria Monocytogenes in complex with a 30-bp operator PrfA-box motif
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LEJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 291 Droplets of 4 microl protein-DNA solution (ratio 1:1.3) in 20 mM Tris-HCl pH 8.0, 50 mM NaCl, and 1 mM EDTA at 6 mg per ml were mixed with 2 microl reservoir solution consisting of 8% PEG 8000, 100 mM sodium citrate pH 4.6, 100 mM Magnesium acetate and 20% glycerol.
Crystal Properties Matthews coefficient Solvent content 2.79 55.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.628 α = 90 b = 78.628 β = 90 c = 265.122 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 100 PIXEL DECTRIS PILATUS3 6M 2017-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.9677 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.9 47.1 99.8 0.137 0.038 18.2 25.7 19313
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3 99.9 0.976 0.261 4 27.8
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 5LEJ 2.9 47.06 1.34 19125 917 98.8 0.2365 0.2339 0.2427 0.29 0.2894
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 17.79 f_angle_d 0.533 f_chiral_restr 0.039 f_bond_d 0.003 f_plane_restr 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3838 Nucleic Acid Atoms 1230 Solvent Atoms 11 Heterogen Atoms 18
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing