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1.83 Angstrom Resolution Crystal Structure of N-terminal Fragment (residues 1-404) of Elongation Factor G from Enterococcus faecalis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5VH6 PDB entry 5VH6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.3 295 12.5 mg/mL protein in 0.5 sodium chloride, 0.01 M Tris, pH 8.3 against screen PEGs II (G6), 15% w/v PEG6000, 5% w/v glycerol, cryoprotectant: reservoir
Crystal Properties Matthews coefficient Solvent content 2.19 43.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.45 α = 90 b = 86.425 β = 90.17 c = 75.442 γ = 90
Symmetry Space Group P 1 21 1
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) 2017-11-02 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) Rrim I (All) 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 1.83 30 99.8 0.046 0.046 0.052 0.025 28.8 4.5 69321 -3 35.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.83 1.86 99.5 0.793 0.793 0.9 0.423 0.774 2.05 4.4
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 PDB entry 5VH6 1.83 28.95 65859 3436 99.66 0.19278 0.19145 0.1988 0.21734 0.2211 RANDOM 48.832
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] -1.19 -0.42 -1.65 2.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.788 r_dihedral_angle_4_deg 13.115 r_dihedral_angle_3_deg 9.891 r_long_range_B_refined 5.183 r_long_range_B_other 5.151 r_scangle_other 2.984 r_dihedral_angle_1_deg 2.873 r_mcangle_it 2.393 r_mcangle_other 2.393 r_scbond_it 1.859
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.788 r_dihedral_angle_4_deg 13.115 r_dihedral_angle_3_deg 9.891 r_long_range_B_refined 5.183 r_long_range_B_other 5.151 r_scangle_other 2.984 r_dihedral_angle_1_deg 2.873 r_mcangle_it 2.393 r_mcangle_other 2.393 r_scbond_it 1.859 r_scbond_other 1.858 r_mcbond_it 1.523 r_mcbond_other 1.522 r_angle_refined_deg 1.371 r_angle_other_deg 0.829 r_chiral_restr 0.084 r_gen_planes_refined 0.021 r_gen_planes_other 0.018 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 5950 Nucleic Acid Atoms Solvent Atoms 378 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MoRDa phasing