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Structure of Response regulator PleD in complex with c-diGMP and pppGpp
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W25
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M NaCl (Salt)
0.05 M Na Cacod 6.5 pH (Buffer)
10 %w/v PEG 4K (Precipitant)
0.5 mM Spermine (Additive)
Crystal Properties Matthews coefficient Solvent content 3.22 61.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.571 α = 90 b = 132.571 β = 90 c = 508.411 γ = 120
Symmetry Space Group P 61 2 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 EIGER X 9M 2023-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.980114 SOLEIL PROXIMA 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 3 48.96 100 0.361 0.366 0.062 0.998 12.6 33.6 54311 71.66
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 3 3.09 100 3.305 3.356 0.58 0.47 32.4
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3 47.53 1.34 54162 2789 99.97 0.1917 0.1897 0.1922 0.2288 0.2317 Random selection 71.79
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 18.5208 f_angle_d 0.8687 f_chiral_restr 0.0492 f_plane_restr 0.0196 f_bond_d 0.0043
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13572 Nucleic Acid Atoms Solvent Atoms 22 Heterogen Atoms 532
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing