☰ Navigation Tabs
Crystal structure of an ancient sequence-reconstructed Elongation factor Tu (node 184)
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% PEG 8000, 20% ethylene glycol,
20 mM each of
1,6-hexanediol,
1-butanol
1-2-propanediol
2-propanol
1,4-butaediol
1,3-propanediol
and 0.1 mM MES/imidazole, pH6.5
Crystal Properties Matthews coefficient Solvent content 2.89 57.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.203 α = 90 b = 106.122 β = 90 c = 112.472 γ = 90
Symmetry Space Group P 21 21 2
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 2018-09-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97625 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 1.8 112.47 99.8 0.055 0.06 0.025 0.999 13.9 5.9 91686
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 1.8 1.83 97.8 1.819 1.993 0.805 0.425 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 1.8 112.47 87124 4510 99.74 0.199 0.1971 0.2076 0.2373 0.2047 RANDOM 43.081
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] 0.64 1.03 -1.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.355 r_dihedral_angle_4_deg 19.587 r_dihedral_angle_3_deg 14.342 r_dihedral_angle_1_deg 6.933 r_angle_refined_deg 2.037 r_angle_other_deg 1.059 r_chiral_restr 0.119 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.355 r_dihedral_angle_4_deg 19.587 r_dihedral_angle_3_deg 14.342 r_dihedral_angle_1_deg 6.933 r_angle_refined_deg 2.037 r_angle_other_deg 1.059 r_chiral_restr 0.119 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5684 Nucleic Acid Atoms Solvent Atoms 450 Heterogen Atoms 58
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Auto-Rickshaw phasing