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Chaetomium thermophilum FAD-dependent oxidoreductase in complex with ABTS
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ZE2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293.15 17 % (w/v) PEG MME 5000, 0.1 M sodium acetate, pH 5.5, 0.16 M magnesium formate, 20 mM MgCl2, 8.5 mM 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid), protein concentration 8 mg/ml
Crystal Properties Matthews coefficient Solvent content 2.36 47.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.589 α = 90 b = 109.799 β = 90 c = 115.982 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 PILATUS 6M 2019-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.97626 PETRA III, EMBL c/o DESY P13 (MX1)
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 1.4 49.343 95.5 0.058 0.067 0.033 0.999 9.2 3.7 223121 -3.7 16.2
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 1.4 1.42 99.8 0.925 1.079 0.542 0.589 1.4 3.8
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-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6ZE2 1.4 49.343 223009 11066 95.246 0.129 0.1291 0.1277 0.1289 0.1718 0.142 random selection 19.125
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] 1.996 -1.229 -0.767
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.582 r_dihedral_angle_4_deg 20.285 r_dihedral_angle_3_deg 11.971 r_dihedral_angle_1_deg 7.03 r_rigid_bond_restr 3.358 r_scbond_it 3.13 r_scbond_other 3.118 r_mcangle_other 2.174 r_mcangle_it 2.169 r_mcbond_it 1.819
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.582 r_dihedral_angle_4_deg 20.285 r_dihedral_angle_3_deg 11.971 r_dihedral_angle_1_deg 7.03 r_rigid_bond_restr 3.358 r_scbond_it 3.13 r_scbond_other 3.118 r_mcangle_other 2.174 r_mcangle_it 2.169 r_mcbond_it 1.819 r_mcbond_other 1.819 r_angle_refined_deg 1.751 r_angle_other_deg 1.523 r_symmetry_nbd_refined 0.226 r_nbd_refined 0.214 r_symmetry_nbd_other 0.189 r_nbd_other 0.187 r_nbtor_refined 0.173 r_symmetry_xyhbond_nbd_refined 0.156 r_xyhbond_nbd_refined 0.139 r_xyhbond_nbd_other 0.122 r_chiral_restr 0.106 r_symmetry_nbtor_other 0.083 r_symmetry_xyhbond_nbd_other 0.082 r_bond_refined_d 0.013 r_gen_planes_refined 0.013 r_metal_ion_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8917 Nucleic Acid Atoms Solvent Atoms 1653 Heterogen Atoms 362
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing