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1.78 Angstrom Resolution Crystal Structure of N-terminal Fragment (residues 1-405) of Elongation Factor G from Haemophilus influenzae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5TV2 PDB entry 5TV2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 295 11.0 mg/mL protein in 0.5 M sodium chloride, 0.01 M Tris-HCl, pH 8.3 against screen: Classics II (F6), 0.2 M ammonium sulfate, 0.1 M Bis-Tris, pH 5.5, 25% w/v PEG3350
Crystal Properties Matthews coefficient Solvent content 2.66 53.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.823 α = 90 b = 88.487 β = 90 c = 130.279 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 CCD MARMOSAIC 300 mm CCD C(111) 2017-08-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rpim I (All) 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 1.78 30 99.9 0.043 0.043 0.018 38.4 6.9 47575 -3 32.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.78 1.81 100 0.797 0.797 0.325 0.832 2.6 6.9
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 PDB entry 5TV2 1.78 29.8 44829 2357 99.84 0.17457 0.17257 0.1817 0.21366 0.2203 RANDOM 43.177
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] 0.75 0.83 -1.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.006 r_dihedral_angle_4_deg 9.541 r_dihedral_angle_3_deg 8.898 r_long_range_B_refined 5.598 r_long_range_B_other 5.389 r_dihedral_angle_1_deg 2.988 r_scangle_other 2.515 r_mcangle_it 1.987 r_mcangle_other 1.986 r_scbond_it 1.532
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.006 r_dihedral_angle_4_deg 9.541 r_dihedral_angle_3_deg 8.898 r_long_range_B_refined 5.598 r_long_range_B_other 5.389 r_dihedral_angle_1_deg 2.988 r_scangle_other 2.515 r_mcangle_it 1.987 r_mcangle_other 1.986 r_scbond_it 1.532 r_scbond_other 1.532 r_angle_refined_deg 1.368 r_mcbond_it 1.234 r_mcbond_other 1.232 r_angle_other_deg 0.864 r_chiral_restr 0.088 r_gen_planes_refined 0.022 r_gen_planes_other 0.019 r_bond_refined_d 0.008 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2941 Nucleic Acid Atoms Solvent Atoms 290 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MoRDa phasing