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Crystal structure of DNA-binding transcriptional activator EvgA from Escherichia coli str. K-12 substr. MG1655
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5F64
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 mixing 2 volumes of the protein (4 mg/ml in 20 mM Tris/HCl, pH 7.0, 200 mM NaCl, 1 mM TCEP) with 0.8 volume of the well solution (0.1 M Bis-Tris Propane, pH 8.5, 1.22 M Ammonium Tartrate) and 0.2 volume of 0.1 M Betaine.
Crystal Properties Matthews coefficient Solvent content 3.9 68.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 164.378 α = 90 b = 109.061 β = 125.39 c = 106.666 γ = 90
Symmetry Space Group C 1 2 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 2023-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 1.0 SSRF BL18U1
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 2.896 46.2 94.7 0.111 0.12 0.046 0.999 12.2 6.8 23189
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 2.896 3.026 81.5 0.853 0.92 0.344 0.812 2.2 7.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.9 46.2 1.35 23177 1997 67.67 0.2043 0.1991 0.1998 0.2592 0.2574
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 17.511 f_angle_d 0.555 f_chiral_restr 0.045 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6294 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data scaling XDS data reduction PHASER phasing