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Crystal structure of an ancient sequence-reconstructed Elongation Factor Tu (node 317)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EFC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 296 0.2 M Lithium citrate tribasic tetrathydrate, 20% w/v PEG 3350, pH 8.4
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.342 α = 90 b = 100.289 β = 90 c = 160.719 γ = 90
Symmetry Space Group C 2 2 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 EIGER X 16M 2019-06-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.918401 MAX IV BioMAX
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 1.68 29.44 98.9 0.093 0.098 0.029 0.999 14.1 11 88432
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 1.68 1.71 83.2 0.834 0.878 0.268 0.785 10
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 1EFC 1.68 29.44 83920 4447 98.8 0.1927 0.1912 0.2013 0.2204 0.2243 RANDOM 24.52
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] -0.38 -0.16 0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.52 r_dihedral_angle_4_deg 15.484 r_dihedral_angle_3_deg 13.35 r_dihedral_angle_1_deg 7.251 r_angle_refined_deg 1.851 r_angle_other_deg 1.458 r_chiral_restr 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.52 r_dihedral_angle_4_deg 15.484 r_dihedral_angle_3_deg 13.35 r_dihedral_angle_1_deg 7.251 r_angle_refined_deg 1.851 r_angle_other_deg 1.458 r_chiral_restr 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5530 Nucleic Acid Atoms Solvent Atoms 363 Heterogen Atoms 58
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Auto-Rickshaw phasing