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The Transcriptional Regulator PrfA from Listeria Monocytogenes in complex with a ring-fused 2-pyridone (MK37)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5F1R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 291 PrfA was co-crystallized with complex (5 mol excess) using the hanging-drop vapor-diffusion technique. Crystals grew in 5 days after 2 microL of the protein solution (3.2-3.5 mg per ml PrfA, 200 mM NaCl, 20 mM NaP buffer, pH 6.5) was mixed with an equal volume of precipitant solution containing 20-24% PEG-4000, 17% isopropanol, 100 mM Na citrate pH 5.5 and allowed to equilibrate over a 1 ml solution of the precipitant in a Linbro plate (Hampton Research).
Crystal Properties Matthews coefficient Solvent content 2.33 47.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.109 α = 90 b = 89.048 β = 90 c = 116.231 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 PILATUS3 2M 2016-05-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.873 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.95 44.524 100 0.068 13.8 5.6 37197
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2 99.9 0.867 1.9 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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5F1R 1.95 44.52 1.34 37194 1847 99.9 0.194 0.192 0.2007 0.236 0.2387
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 13.205 f_angle_d 0.859 f_chiral_restr 0.052 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3779 Nucleic Acid Atoms Solvent Atoms 191 Heterogen Atoms 40
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHENIX phasing