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FAD-dependent oxidoreductase from Chaetomium thermophilum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4YNT
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 cystamine, protein concentration 8 mg/ml
Crystal Properties Matthews coefficient Solvent content 2.37 48.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.654 α = 90 b = 116.774 β = 90.797 c = 109.903 γ = 90
Symmetry Space Group P 1 21 1
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 2016-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 1.0332 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 1.31 46.69 95.4 0.045 0.053 0.029 0.999 11.2 3.2 268173 -3.7 12.7
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 1.31 1.33 96.8 0.489 0.599 0.34 0.795 2 2.8
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 4YNT 1.31 46.69 268125 5346 95.348 0.107 0.1072 0.1059 0.1074 0.137 0.1157 random selection 17.369
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] 0.568 0.293 0.335 -0.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.992 r_dihedral_angle_4_deg 18.812 r_dihedral_angle_3_deg 11.281 r_dihedral_angle_1_deg 6.958 r_rigid_bond_restr 3.354 r_lrange_it 3.215 r_scangle_it 2.907 r_scangle_other 2.907 r_lrange_other 2.871 r_scbond_it 2.541
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.992 r_dihedral_angle_4_deg 18.812 r_dihedral_angle_3_deg 11.281 r_dihedral_angle_1_deg 6.958 r_rigid_bond_restr 3.354 r_lrange_it 3.215 r_scangle_it 2.907 r_scangle_other 2.907 r_lrange_other 2.871 r_scbond_it 2.541 r_scbond_other 2.541 r_mcangle_other 2.009 r_mcangle_it 2.007 r_angle_refined_deg 1.825 r_mcbond_it 1.655 r_mcbond_other 1.655 r_angle_other_deg 1.572 r_nbd_refined 0.219 r_nbd_other 0.211 r_symmetry_xyhbond_nbd_refined 0.192 r_symmetry_nbd_other 0.191 r_symmetry_nbd_refined 0.179 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.138 r_chiral_restr 0.109 r_symmetry_nbtor_other 0.085 r_symmetry_xyhbond_nbd_other 0.061 r_bond_refined_d 0.013 r_gen_planes_refined 0.013 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8922 Nucleic Acid Atoms Solvent Atoms 1664 Heterogen Atoms 267
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MoRDa phasing