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X-ray structure of the Thermus thermophilus Q218E mutant of the PilF-GSPIIB domain in the c-di-GMP bound state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8PDK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 291 1.5 M LiSO4
0.1 M NaAc pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.98 58.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.099 α = 90 b = 108.099 β = 90 c = 86.183 γ = 120
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 16M 2021-08-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.976 PETRA III, EMBL c/o DESY P13 (MX1)
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 1.55 41.13 99.98 0.08074 0.08503 0.02645 0.997 12.78 12.78 54531 31.17
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.605 0.594
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.55 41.13 1.96 54526 1771 99.99 0.1844 0.1837 0.2029 0.2372 42.46
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 36.0483 f_angle_d 1.1585 f_chiral_restr 0.0641 f_bond_d 0.006 f_plane_restr 0.0051
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2226 Nucleic Acid Atoms Solvent Atoms 287 Heterogen Atoms 43
Software Software Software Name Purpose PHENIX refinement MxCuBE data collection autoPROC data processing XDS data reduction XDS data scaling Coot model building PHENIX phasing