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2.60 Angstrom Resolution Crystal Structure of Elongation Factor G 2 from Pseudomonas putida.
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 7 292 Protein: 9.5 mg/ml, 0.01M Tris HCl (pH 8.3);
Screen: PACT (C10), 0.2M Magnesium chloride, 0.1M HEPES (pH 7.0), 20% (w/v) PEG 6000.
Crystal Properties Matthews coefficient Solvent content 2.41 49.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.434 α = 90 b = 79.968 β = 94.21 c = 183.516 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) 2017-04-20 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 30 100 0.078 0.078 0.041 17.3 4.4 44241 -3 65.9
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 2.6 2.64 100 0.804 0.804 0.912 0.427 0.742 1.9 4.5
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 2.6 29.83 41967 2120 99.91 0.22517 0.22316 0.2211 0.26393 0.2581 RANDOM 71.367
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] -2.06 1.04 4.46 -2.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 12.598 r_dihedral_angle_4_deg 7.327 r_long_range_B_refined 7.091 r_long_range_B_other 7.084 r_dihedral_angle_3_deg 6.857 r_scangle_other 4.425 r_mcangle_it 4.034 r_mcangle_other 4.034 r_scbond_it 2.708 r_scbond_other 2.708
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 12.598 r_dihedral_angle_4_deg 7.327 r_long_range_B_refined 7.091 r_long_range_B_other 7.084 r_dihedral_angle_3_deg 6.857 r_scangle_other 4.425 r_mcangle_it 4.034 r_mcangle_other 4.034 r_scbond_it 2.708 r_scbond_other 2.708 r_mcbond_it 2.426 r_mcbond_other 2.425 r_dihedral_angle_1_deg 1.478 r_angle_refined_deg 1.168 r_angle_other_deg 0.292 r_gen_planes_refined 0.053 r_chiral_restr 0.049 r_gen_planes_other 0.049 r_bond_refined_d 0.003 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 10509 Nucleic Acid Atoms Solvent Atoms 116 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing