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X-ray structure of the CeuE Homologue from Parageobacillus thermoglucosidasius - azotochelin 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 4 293 25% PEG 1500; 0.1 M PCMB pH 4.0 (Na propionate: Na cacodylate: BisTris propane 2:1:2). LIgand: 5mM Fe(III) Azotochelin (Washed) 1:10 ratio protein:ligand.
Crystal Properties Matthews coefficient Solvent content 2.29 46.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.295 α = 90 b = 116.711 β = 90 c = 141.471 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 2020-08-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.979499 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 1.969 70.836 100 0.069 0.074 0.028 1 16.4 12.8 21889
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 1.97 2.02 2.703 2.922 1.1 0.408 13.3
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 1.969 70.836 21853 1084 99.963 0.207 0.2048 0.2044 0.2547 0.2533 59.941
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] 0.03 -0.871 0.841
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.939 r_dihedral_angle_6_deg 16.504 r_dihedral_angle_2_deg 7.528 r_dihedral_angle_1_deg 7.095 r_lrange_it 6.146 r_lrange_other 6.14 r_scangle_other 4.979 r_scangle_it 4.976 r_scbond_it 3.511 r_scbond_other 3.506
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.939 r_dihedral_angle_6_deg 16.504 r_dihedral_angle_2_deg 7.528 r_dihedral_angle_1_deg 7.095 r_lrange_it 6.146 r_lrange_other 6.14 r_scangle_other 4.979 r_scangle_it 4.976 r_scbond_it 3.511 r_scbond_other 3.506 r_mcangle_it 3.315 r_mcangle_other 3.314 r_mcbond_it 2.538 r_mcbond_other 2.538 r_angle_refined_deg 1.348 r_angle_other_deg 0.55 r_symmetry_nbd_refined 0.429 r_symmetry_xyhbond_nbd_refined 0.332 r_nbd_refined 0.231 r_xyhbond_nbd_refined 0.222 r_symmetry_nbd_other 0.191 r_nbd_other 0.181 r_nbtor_refined 0.179 r_symmetry_nbtor_other 0.08 r_symmetry_metal_ion_refined 0.063 r_chiral_restr 0.058 r_bond_other_d 0.015 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_gen_planes_other 0.001 r_metal_ion_refined
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2167 Nucleic Acid Atoms Solvent Atoms 29 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing