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Crystal structure of radical SAM epimerase EpeE from Bacillus subtilis with [4Fe-4S] clusters, S-adenosyl-L-homocysteine and RiPP peptide 5 bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Fe-SAD Exprimental model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 14% (w/v) PEG 1000, Tris 0.1 M
Crystal Properties Matthews coefficient Solvent content 2.82 56.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.73 α = 90 b = 92.37 β = 90 c = 126.72 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 PIXEL DECTRIS EIGER X 16M KB Mirrors 2021-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.97857 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.39 46.19 99.9 0.118 0.122 0.031 0.999 14.8 15.2 571609
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.39 2.48 1.411 1.458 0.366 0.84 1.9
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 Fe-SAD Exprimental model 2.393 46.19 37607 1881 99.9 0.1879 0.1861 0.1813 0.2222 0.2224 RANDOM 63.94
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] -10.168 7.7799 2.3881
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.56 t_omega_torsion 2.97 t_angle_deg 0.93 t_bond_d 0.008 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_sum_occupancies t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5381 Nucleic Acid Atoms Solvent Atoms 210 Heterogen Atoms 204
Software Software Software Name Purpose BUSTER refinement XDS data reduction XDS data scaling PHASER phasing MxCuBE data collection