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Crystal structure of a fragment (1-405) of an elongation factor G from Vibrio vulnificus CMCP6
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 5 293 0.1 MMT buffer, 25 % PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.1 41.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.678 α = 90 b = 54.496 β = 116.58 c = 65.319 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 225 mm CCD 3.0 Undulator 2016-10-05 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) CC (Half) 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 1.6 30 97.8 0.05 0.75 31.3 6.4 48492
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 100 0.73 2.1 4.3 2460
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4fn5 1.6 30 46069 2405 97.44 0.18232 0.17864 0.25307 0.293 RANDOM 38.817
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] -1.08 -2.01 2.8 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.84 r_sphericity_bonded 18.566 r_dihedral_angle_4_deg 12.734 r_dihedral_angle_3_deg 11.253 r_scangle_other 6.828 r_long_range_B_refined 6.605 r_long_range_B_other 6.56 r_scbond_it 6.088 r_scbond_other 6.07 r_mcangle_it 4.996
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.84 r_sphericity_bonded 18.566 r_dihedral_angle_4_deg 12.734 r_dihedral_angle_3_deg 11.253 r_scangle_other 6.828 r_long_range_B_refined 6.605 r_long_range_B_other 6.56 r_scbond_it 6.088 r_scbond_other 6.07 r_mcangle_it 4.996 r_mcangle_other 4.995 r_rigid_bond_restr 4.287 r_mcbond_other 4.269 r_mcbond_it 4.257 r_dihedral_angle_1_deg 3.419 r_angle_refined_deg 1.782 r_angle_other_deg 0.977 r_chiral_restr 0.118 r_gen_planes_refined 0.019 r_bond_refined_d 0.015 r_gen_planes_other 0.014 r_bond_other_d 0.002 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_sphericity_free
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2862 Nucleic Acid Atoms Solvent Atoms 247 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PHENIX phasing HKL-2000 data reduction