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X-ray structure of the CeuE Homologue from Parageobacillus thermoglucosidasius - apo form
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 6.5 293 17% PEG 3350; 0.1M MES, pH 6.5, 0.1M MgAc; Cryo- EthGl
Crystal Properties Matthews coefficient Solvent content 2.26 45.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.369 α = 90 b = 118.433 β = 90 c = 141.046 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 X 16M 2021-02-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976300 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 2.13 70.623 100 0.069 0.074 0.028 1 17.8 12.7 17078
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 2.13 2.19 3.272 3.543 1.352 0.377 12.9
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 (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 2.133 70.623 17045 862 99.93 0.224 0.2216 0.2216 0.2661 0.2676 76.498
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] 1.572 0.088 -1.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.985 r_dihedral_angle_6_deg 14.585 r_lrange_it 10.572 r_lrange_other 10.572 r_scangle_it 8.103 r_dihedral_angle_1_deg 8.1 r_scangle_other 7.825 r_mcangle_it 6.954 r_mcangle_other 6.952 r_scbond_it 5.681
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.985 r_dihedral_angle_6_deg 14.585 r_lrange_it 10.572 r_lrange_other 10.572 r_scangle_it 8.103 r_dihedral_angle_1_deg 8.1 r_scangle_other 7.825 r_mcangle_it 6.954 r_mcangle_other 6.952 r_scbond_it 5.681 r_scbond_other 5.414 r_mcbond_it 4.962 r_mcbond_other 4.96 r_dihedral_angle_2_deg 2.305 r_angle_refined_deg 1.246 r_symmetry_nbd_refined 0.447 r_angle_other_deg 0.388 r_symmetry_metal_ion_refined 0.324 r_symmetry_xyhbond_nbd_refined 0.29 r_nbd_refined 0.234 r_nbd_other 0.224 r_xyhbond_nbd_refined 0.207 r_symmetry_nbd_other 0.189 r_nbtor_refined 0.179 r_symmetry_nbtor_other 0.08 r_symmetry_xyhbond_nbd_other 0.07 r_chiral_restr 0.052 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2167 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing