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The Transcriptional Regulator PrfA-A218G mutant from Listeria Monocytogenes
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 Droplets of 2 to 4 microl protein solution in 50 mM sodium phosphate pH 6.5 and 200 mM NaCl at 3 mg per ml were mixed with 2 microl reservoir solution consisting of 22-25% PEG 4000, 100 mM sodium citrate pH 5.5, and 17%
Crystal Properties Matthews coefficient Solvent content 2.23 44.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.837 α = 90 b = 88.021 β = 90 c = 116.386 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 EIGER X 4M 2018-02-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9680 ESRF MASSIF-3
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 2.6 48.6 99.9 0.231 0.093 10.3 13.4 15707
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 2.6 2.7 99.9 1.86 0.742 1.8 13.9
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 2.6 48.543 1.33 15680 745 99.66 0.1817 0.1781 0.1855 0.2544 0.2548
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 11.031 f_angle_d 0.445 f_chiral_restr 0.04 f_bond_d 0.002 f_plane_restr 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3787 Nucleic Acid Atoms Solvent Atoms 203 Heterogen Atoms 18
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing