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2.6 Angstrom Resolution Crystal Structure of N-terminal Fragment (residues 1-406) of Elongation Factor G from Bacillus subtilis.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XEX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 295 Protein: 8.0 mg/ml, 0.01M Tris HCl (pH 8.3); Screen: PACT (B7), 0.2M Sodium chloride, 0.1M MES pH (6.0), 20% (w/v) PEG 6000.
Crystal Properties Matthews coefficient Solvent content 2.2 43.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.672 α = 90 b = 56.672 β = 90 c = 248.722 γ = 90
Symmetry Space Group P 43 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 CCD MARMOSAIC 300 mm CCD C(111) 2017-03-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 2.6 30 99.8 0.093 0.093 0.038 18.5 6.8 13280 -3 59.2
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 2.6 2.64 100 0.796 0.796 0.333 0.867 2.2 6.4
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 2XEX 2.61 28.81 12544 661 99.59 0.22811 0.22542 0.2264 0.27732 0.2737 RANDOM 75.252
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] 3.79 3.79 -7.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.042 r_dihedral_angle_4_deg 9.092 r_dihedral_angle_3_deg 7.102 r_long_range_B_refined 5.613 r_long_range_B_other 5.612 r_mcangle_it 3.324 r_mcangle_other 3.324 r_scangle_other 2.626 r_mcbond_it 1.851 r_mcbond_other 1.844
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.042 r_dihedral_angle_4_deg 9.092 r_dihedral_angle_3_deg 7.102 r_long_range_B_refined 5.613 r_long_range_B_other 5.612 r_mcangle_it 3.324 r_mcangle_other 3.324 r_scangle_other 2.626 r_mcbond_it 1.851 r_mcbond_other 1.844 r_dihedral_angle_1_deg 1.57 r_scbond_it 1.44 r_scbond_other 1.439 r_angle_refined_deg 1.238 r_angle_other_deg 0.809 r_chiral_restr 0.068 r_gen_planes_refined 0.021 r_gen_planes_other 0.018 r_bond_refined_d 0.006 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 2933 Nucleic Acid Atoms Solvent Atoms 63 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing