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Flavin mononucleotide-dependent nitroreductase B.thetaiotaomicron (BT_1316)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.2 293 20% (v/v) PEG 1000, 0.1M citrate phosphate buffer
Crystal Properties Matthews coefficient Solvent content 2.04 39.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.626 α = 90 b = 65.333 β = 90 c = 90.543 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 EIGER X 16M 2021-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.976200 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 2.2 90.54 100 0.118 0.122 0.032 0.999 21 26.3 17692
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 2.2 2.27 0.387 0.402 0.106 0.989 26.7
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE AF-Q8A858-F1 2.2 52.981 17632 854 99.915 0.169 0.1664 0.1665 0.2209 0.2223 30.37
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] -2.755 0.396 2.359
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.307 r_dihedral_angle_6_deg 16.616 r_dihedral_angle_2_deg 10.562 r_lrange_it 9.604 r_lrange_other 9.595 r_scangle_it 8.171 r_scangle_other 8.169 r_dihedral_angle_1_deg 6.863 r_scbond_other 5.651 r_scbond_it 5.648
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.307 r_dihedral_angle_6_deg 16.616 r_dihedral_angle_2_deg 10.562 r_lrange_it 9.604 r_lrange_other 9.595 r_scangle_it 8.171 r_scangle_other 8.169 r_dihedral_angle_1_deg 6.863 r_scbond_other 5.651 r_scbond_it 5.648 r_mcangle_it 4.496 r_mcangle_other 4.495 r_mcbond_it 3.202 r_mcbond_other 3.202 r_angle_refined_deg 1.879 r_angle_other_deg 0.605 r_nbd_refined 0.219 r_symmetry_nbd_refined 0.198 r_symmetry_nbd_other 0.184 r_nbtor_refined 0.177 r_nbd_other 0.161 r_xyhbond_nbd_refined 0.151 r_ncsr_local_group_1 0.115 r_chiral_restr 0.091 r_symmetry_xyhbond_nbd_refined 0.083 r_symmetry_nbtor_other 0.082 r_symmetry_xyhbond_nbd_other 0.017 r_bond_refined_d 0.014 r_gen_planes_refined 0.013 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2564 Nucleic Acid Atoms Solvent Atoms 119 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing