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Complex structure of AMPylated EF-Tu-T62A bound to SoFic-H198A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EQX SoFic experimental model Other EF-Tu structure that was solved in the same study
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 294 0.1 M Tris-HCl (pH 8.5), 8 % (v/v) PEG 8000
Crystal Properties Matthews coefficient Solvent content 3.29 62.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.843 α = 112.9 b = 95.942 β = 100.62 c = 100.17 γ = 90.43
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 EIGER2 X CdTe 16M 2024-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.97625 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.76 90.352 88.3 0.06 0.998 6 3.6 29290 82.41
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.764 3.141 56.8 0.625 0.657 1.6 3.8
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 2.76 33.03 1.97 29249 1421 50.88 0.196 0.1943 0.194 0.2292 0.2266 86.05
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 10.2627 f_angle_d 0.4775 f_chiral_restr 0.0407 f_plane_restr 0.0033 f_bond_d 0.0015
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11536 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms 102
Software Software Software Name Purpose MxCuBE data collection STARANISO data scaling Aimless data scaling XDS data reduction autoPROC data processing PHASER phasing Coot model building PHENIX refinement