☰ Navigation Tabs
FAD-dependent oxidoreductase from Chaetomium thermophilum in complex with fragment 4-oxo-N-[(1S)-1-(pyridin-3-yl)ethyl]-4-(thiophen-2-yl)butanamide
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, protein concentration 8 mg/ml
Crystal Properties Matthews coefficient Solvent content 2.36 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.562 α = 90 b = 109.875 β = 90 c = 116.113 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 2018-05-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
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 1.6 49.38 93.5 0.088 0.097 0.039 0.998 8.7 5.5 147085 -3.7 16.8
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 1.6 1.63 98.5 1.009 1.108 0.441 0.659 1.6 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6ZE2 1.6 49.38 146842 7299 93.091 0.172 0.1722 0.1697 0.2022 0.1731 random selection 19.643
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] 1.458 -0.984 -0.474
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.092 r_dihedral_angle_4_deg 18.158 r_dihedral_angle_3_deg 11.87 r_dihedral_angle_1_deg 7.223 r_lrange_it 4.372 r_lrange_other 4.001 r_scangle_it 2.901 r_scangle_other 2.901 r_scbond_it 1.978 r_scbond_other 1.976
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.092 r_dihedral_angle_4_deg 18.158 r_dihedral_angle_3_deg 11.87 r_dihedral_angle_1_deg 7.223 r_lrange_it 4.372 r_lrange_other 4.001 r_scangle_it 2.901 r_scangle_other 2.901 r_scbond_it 1.978 r_scbond_other 1.976 r_mcangle_other 1.785 r_mcangle_it 1.784 r_angle_refined_deg 1.653 r_angle_other_deg 1.377 r_mcbond_it 1.343 r_mcbond_other 1.343 r_nbd_refined 0.202 r_symmetry_xyhbond_nbd_refined 0.195 r_symmetry_nbd_other 0.184 r_nbd_other 0.178 r_nbtor_refined 0.166 r_symmetry_nbd_refined 0.16 r_xyhbond_nbd_refined 0.146 r_chiral_restr 0.089 r_symmetry_nbtor_other 0.08 r_symmetry_xyhbond_nbd_other 0.07 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8917 Nucleic Acid Atoms Solvent Atoms 1601 Heterogen Atoms 340
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing