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2.22 Angstrom Crystal Structure of N-terminal Fragment (residues 1-419) of Elongation Factor G from Legionella pneumophila.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FN5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 295 Protein: 9.4 mg/ml, 0.01M Tris HCl (pH 8.3);
Screen: JCSG+ (C4), 0.1M HEPES (pH 6.5), 10% (w/v) PEG 6000;
Cryo: Screen solution + 50% Sucrose, (1:1)
Crystal Properties Matthews coefficient Solvent content 2.99 58.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.399 α = 90 b = 89.853 β = 90 c = 117.98 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 CCD MARMOSAIC 300 mm CCD C(111) 2016-11-15 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) 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 2.22 30 99.9 0.08 0.08 24.1 7.3 28863 -3 40.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.22 2.26 99.4 0.659 0.861 3.2 7.4
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 4FN5 2.22 29.87 27321 1417 99.85 0.16625 0.16479 0.1724 0.19546 0.2 RANDOM 44.86
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] 2.48 -0.99 -1.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.64 r_dihedral_angle_4_deg 11.404 r_dihedral_angle_3_deg 9.908 r_long_range_B_refined 6.926 r_long_range_B_other 6.754 r_scangle_other 4.631 r_mcangle_other 3.139 r_mcangle_it 3.132 r_dihedral_angle_1_deg 2.903 r_scbond_it 2.837
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.64 r_dihedral_angle_4_deg 11.404 r_dihedral_angle_3_deg 9.908 r_long_range_B_refined 6.926 r_long_range_B_other 6.754 r_scangle_other 4.631 r_mcangle_other 3.139 r_mcangle_it 3.132 r_dihedral_angle_1_deg 2.903 r_scbond_it 2.837 r_scbond_other 2.836 r_mcbond_it 1.98 r_mcbond_other 1.954 r_angle_refined_deg 1.444 r_angle_other_deg 0.837 r_chiral_restr 0.084 r_gen_planes_refined 0.022 r_gen_planes_other 0.018 r_bond_refined_d 0.009 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 2965 Nucleic Acid Atoms Solvent Atoms 218 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHENIX phasing