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Crystal structure of an ancient sequence-reconstructed Elongation Factor Tu (node 262)
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 10% w/v PEG 4000, 20% v/v glycerol 0.03M of each ethylene glycol (0.3M diethyleneglycol, 0.3M
triethyleneglycol, 0.3M tetraethyleneglycol, 0.3M pentaethyleneglycol), 0.1M MOPS/HEPES-Na pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.83 56.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.944 α = 90 b = 73.691 β = 90 c = 113.756 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 PILATUS3 6M 2018-04-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.07227 ESRF ID29
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 61.85 99.1 0.11 0.116 0.036 0.998 13.9 10.4 33001
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 1.052 1.111 0.351 0.813 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 1EFC 2 61.85 31282 1674 98.91 0.1815 0.1786 0.1874 0.2334 0.2336 RANDOM 35.594
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] -1.12 3.52 -2.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.791 r_dihedral_angle_4_deg 20.636 r_dihedral_angle_3_deg 15.211 r_dihedral_angle_1_deg 6.43 r_angle_refined_deg 1.946 r_angle_other_deg 1.031 r_chiral_restr 0.119 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.791 r_dihedral_angle_4_deg 20.636 r_dihedral_angle_3_deg 15.211 r_dihedral_angle_1_deg 6.43 r_angle_refined_deg 1.946 r_angle_other_deg 1.031 r_chiral_restr 0.119 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2916 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 29
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Auto-Rickshaw phasing