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X-ray structure of the CeuE Homologue from Geobacillus stearothermophilus - 5-LICAM siderophore analogue complex.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8PBX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Morpheus A12: 12.5% PEG 1000, 12.5% PEG 3350, 12.5% MPD, 0.03M of each divalent cation (MgCl2, CaCl2), 0.1M Bicine/Trizma base pH 8.5 5mM Fe(III) 5-LICAM 1:10 ratio protein:ligand. No cryo.
Crystal Properties Matthews coefficient Solvent content 2.07 40.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.395 α = 90 b = 34.432 β = 92.889 c = 119.109 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 PIXEL DECTRIS EIGER2 S 16M 2020-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.93622 Diamond I03
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 1.47 67.4 99.8 0.04 0.048 0.026 0.999 14.6 6.5 93663
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 1.47 1.5 2.86 3.423 1.86 0.432 6.3
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 8PBX 1.471 67.4 93643 4698 99.791 0.182 0.1797 0.1792 0.2326 0.2344 42.224
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] 2.02 -1.192 -1.941 0.042
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.302 r_dihedral_angle_6_deg 15.281 r_lrange_other 9.142 r_lrange_it 9.141 r_scangle_it 9.136 r_scangle_other 9.135 r_rigid_bond_restr 8.281 r_scbond_it 8.127 r_scbond_other 8.125 r_mcangle_it 8.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.302 r_dihedral_angle_6_deg 15.281 r_lrange_other 9.142 r_lrange_it 9.141 r_scangle_it 9.136 r_scangle_other 9.135 r_rigid_bond_restr 8.281 r_scbond_it 8.127 r_scbond_other 8.125 r_mcangle_it 8.012 r_mcangle_other 8.012 r_mcbond_it 7.861 r_mcbond_other 7.852 r_dihedral_angle_1_deg 6.326 r_dihedral_angle_2_deg 3.784 r_angle_refined_deg 1.345 r_angle_other_deg 0.464 r_symmetry_nbd_refined 0.243 r_nbd_refined 0.225 r_symmetry_xyhbond_nbd_refined 0.215 r_xyhbond_nbd_refined 0.214 r_symmetry_nbd_other 0.189 r_nbd_other 0.181 r_nbtor_refined 0.178 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.067 r_symmetry_xyhbond_nbd_other 0.053 r_xyhbond_nbd_other 0.051 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4357 Nucleic Acid Atoms Solvent Atoms 202 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing