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Crystal structure of an ancient sequence-reconstructed Elongation factor Tu (node 170)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DG1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 296 0.2 M Potassium Chloride, 20% w/v Polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.99 58.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.225 α = 90 b = 73.956 β = 90 c = 115.12 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS 6M 2018-09-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97242 ESRF ID23-1
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 45.42 99 0.052 0.055 0.018 0.999 17.5 9.7 33564
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 2.05 96.5 1.596 1.686 0.534 0.724 9.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 THROUGHOUT 1DG1 2 45.42 31782 1723 98.82 0.1949 0.1923 0.2045 0.2417 0.1979 RANDOM 66.933
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] -3.78 9.19 -5.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.278 r_dihedral_angle_4_deg 21.394 r_dihedral_angle_3_deg 17.272 r_dihedral_angle_1_deg 7.661 r_angle_refined_deg 1.983 r_angle_other_deg 1.122 r_chiral_restr 0.114 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.278 r_dihedral_angle_4_deg 21.394 r_dihedral_angle_3_deg 17.272 r_dihedral_angle_1_deg 7.661 r_angle_refined_deg 1.983 r_angle_other_deg 1.122 r_chiral_restr 0.114 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2800 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction Auto-Rickshaw phasing