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X-ray structure of the CeuE Homologue from Geobacillus stearothermophilus - azotochelin complex.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8BPX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Morph C8: 12.5% PEG1K; 12.5% PEG 3350; 12.5% MPD; 0.03M each NPS (NaNO3, Na2HPO4, (NH4)2SO4); 0.1M MOPS/HEPES pH7.5. Ligand: 1.67mM Fe azotochelin-sulf/pyr-Ir catalyst, 1:1 protein:ligand ratio.
Crystal Properties Matthews coefficient Solvent content 2 38.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.158 α = 90 b = 66.652 β = 90 c = 117.055 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 EIGER2 S 16M 2022-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97628 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 1.38 58.596 97.5 0.128 0.138 0.051 0.998 8.2 13.6 54541
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 1.38 1.4 4.439 4.775 1.752 0.473 14.2
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 8BPX 1.38 58.596 54461 2753 97.353 0.217 0.2141 0.2128 0.2622 0.2608 30.655
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] -3.51 -4.427 7.937
RMS Deviations Key Refinement Restraint Deviation r_rigid_bond_restr 22.582 r_dihedral_angle_6_deg 15.601 r_dihedral_angle_3_deg 14.992 r_lrange_other 7.391 r_lrange_it 7.386 r_scangle_it 7.301 r_scangle_other 7.299 r_mcangle_other 6.837 r_mcangle_it 6.834 r_scbond_other 6.831
RMS Deviations Key Refinement Restraint Deviation r_rigid_bond_restr 22.582 r_dihedral_angle_6_deg 15.601 r_dihedral_angle_3_deg 14.992 r_lrange_other 7.391 r_lrange_it 7.386 r_scangle_it 7.301 r_scangle_other 7.299 r_mcangle_other 6.837 r_mcangle_it 6.834 r_scbond_other 6.831 r_scbond_it 6.828 r_dihedral_angle_1_deg 6.54 r_mcbond_it 5.826 r_mcbond_other 5.805 r_dihedral_angle_2_deg 3.345 r_angle_refined_deg 1.395 r_angle_other_deg 0.513 r_nbd_refined 0.231 r_nbd_other 0.222 r_symmetry_xyhbond_nbd_refined 0.215 r_symmetry_nbd_other 0.196 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.177 r_symmetry_nbd_refined 0.132 r_xyhbond_nbd_other 0.083 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.07 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_gen_planes_other 0.005 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2214 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing