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FAD-dependent oxidoreductase from Chaetomium thermophilum in complex with fragment 4-nitrocatechol
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, protein concentration 8 mg/ml
Crystal Properties Matthews coefficient Solvent content 2.36 47.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.565 α = 90 b = 109.746 β = 90 c = 116.071 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 2M 2019-01-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.9184 BESSY 14.2
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 1.26 29.063 98.3 0.06 0.065 0.024 1 16.5 7.4 314691 -3.7 10
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 1.26 1.28 91 0.978 1.076 0.439 0.66 1.7 5.7
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 1.26 29.063 314581 6192 98.218 0.114 0.1144 0.11296 0.1146 0.14714 0.1224 random selection 14.313
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] 0.56 -0.477 -0.082
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.764 r_dihedral_angle_1_deg 19.926 r_dihedral_angle_4_deg 19.097 r_dihedral_angle_3_deg 11.108 r_rigid_bond_restr 2.779 r_scangle_other 2.573 r_scangle_it 2.572 r_lrange_other 2.484 r_scbond_it 2.212 r_scbond_other 2.205
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.764 r_dihedral_angle_1_deg 19.926 r_dihedral_angle_4_deg 19.097 r_dihedral_angle_3_deg 11.108 r_rigid_bond_restr 2.779 r_scangle_other 2.573 r_scangle_it 2.572 r_lrange_other 2.484 r_scbond_it 2.212 r_scbond_other 2.205 r_angle_refined_deg 1.839 r_angle_other_deg 1.577 r_mcangle_other 1.529 r_mcangle_it 1.527 r_mcbond_it 1.246 r_mcbond_other 1.246 r_nbd_refined 0.219 r_nbd_other 0.193 r_symmetry_nbd_other 0.186 r_nbtor_refined 0.179 r_symmetry_xyhbond_nbd_refined 0.176 r_xyhbond_nbd_refined 0.152 r_symmetry_xyhbond_nbd_other 0.133 r_chiral_restr 0.118 r_symmetry_nbd_refined 0.102 r_symmetry_nbtor_other 0.09 r_bond_refined_d 0.014 r_gen_planes_refined 0.013 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8917 Nucleic Acid Atoms Solvent Atoms 1884 Heterogen Atoms 349
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing