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X-ray structure of the CeuE Homologue from Parageobacillus thermoglucosidasius - 5LICAM complex.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8BF6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 Opt 17. E9. 18% PEG 3350, 0.1M TRIS, pH8.5, 0.05M ZnAc, Cryo ethylene glycol. Ligand: 5mM Fe(III) 5-LICAM 1:10 ratio protein:ligand.
Crystal Properties Matthews coefficient Solvent content 2.29 46.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.063 α = 90 b = 117.392 β = 90 c = 141.712 γ = 90
Symmetry Space Group C 2 2 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 2022-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976238 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 2.069 36.83 99.7 0.101 0.105 0.029 0.988 13.3 23.1 18904
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 2.07 2.13 3.363 3.648 1.396 0.238 13
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 8BF6 2.069 36.827 18840 938 99.493 0.213 0.2097 0.2096 0.2656 0.2642 84.136
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] 3.691 -4.534 0.843
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.912 r_dihedral_angle_6_deg 14.707 r_dihedral_angle_1_deg 7.099 r_lrange_it 6.825 r_lrange_other 6.825 r_dihedral_angle_2_deg 5.789 r_scangle_it 5.096 r_scangle_other 5.034 r_mcangle_it 4.361 r_mcangle_other 4.359
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.912 r_dihedral_angle_6_deg 14.707 r_dihedral_angle_1_deg 7.099 r_lrange_it 6.825 r_lrange_other 6.825 r_dihedral_angle_2_deg 5.789 r_scangle_it 5.096 r_scangle_other 5.034 r_mcangle_it 4.361 r_mcangle_other 4.359 r_scbond_it 3.636 r_scbond_other 3.456 r_mcbond_it 3.285 r_mcbond_other 3.285 r_angle_refined_deg 1.25 r_symmetry_nbd_refined 0.523 r_angle_other_deg 0.419 r_symmetry_xyhbond_nbd_refined 0.31 r_nbd_refined 0.241 r_symmetry_nbd_other 0.193 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.165 r_nbd_other 0.122 r_symmetry_metal_ion_refined 0.096 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.059 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2167 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing