☰ Navigation Tabs
X-ray structure of the Thermus thermophilus Q190E 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 1.6M LiSO4
0.1 M Sodiumacetate pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.98 58.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.966 α = 90 b = 107.966 β = 90 c = 86.366 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 1.9 32.71 99.97 0.1055 0.1109 0.034 0.997 10.12 10.4 29580 44.9
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 1.9 1.968 0.636
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 1.9 32.71 1.96 29574 3243 99.94 0.1944 0.1926 0.1935 0.2251 0.2274 58.77
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 38.1582 f_angle_d 1.0642 f_chiral_restr 0.0529 f_bond_d 0.0064 f_plane_restr 0.0055
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2208 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 46
Software Software Software Name Purpose MxCuBE data collection autoPROC data processing PHENIX phasing autoPROC data scaling Coot model building PHENIX refinement XDS data scaling XDS data reduction