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Flavin mononucleotide-dependent nitroreductase B.thetaiotaomicron (BT_0217)
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 5.5 293 12mM sodium nitrate, 12mM sodium phosphate, 12mM ammonium sulphate
Crystal Properties Matthews coefficient Solvent content 1.97 37.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.03 α = 90 b = 44.41 β = 110.739 c = 103.04 γ = 90
Symmetry Space Group C 1 2 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 EIGER X 16M 2021-04-20 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 1.7 38.193 99.1 0.184 0.202 0.081 0.994 9.7 10.4 37180
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 1.7 1.73 0.534 0.716 0.471 0.813 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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE AF-Q8AB93-F1 1.7 38.193 37180 1777 99.07 0.151 0.1492 0.1492 0.182 0.1825 22.224
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] -0.871 0.225 -0.131 0.646
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.536 r_dihedral_angle_6_deg 15.365 r_dihedral_angle_2_deg 7.965 r_lrange_it 6.284 r_dihedral_angle_1_deg 6.28 r_lrange_other 6.266 r_scangle_it 5.633 r_scangle_other 5.549 r_scbond_it 3.766 r_scbond_other 3.708
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.536 r_dihedral_angle_6_deg 15.365 r_dihedral_angle_2_deg 7.965 r_lrange_it 6.284 r_dihedral_angle_1_deg 6.28 r_lrange_other 6.266 r_scangle_it 5.633 r_scangle_other 5.549 r_scbond_it 3.766 r_scbond_other 3.708 r_mcangle_it 2.809 r_mcangle_other 2.809 r_mcbond_it 2.076 r_mcbond_other 2.076 r_angle_refined_deg 1.91 r_angle_other_deg 0.658 r_symmetry_xyhbond_nbd_refined 0.271 r_symmetry_nbd_refined 0.233 r_nbd_refined 0.227 r_nbd_other 0.19 r_nbtor_refined 0.18 r_symmetry_nbd_other 0.177 r_symmetry_xyhbond_nbd_other 0.175 r_xyhbond_nbd_refined 0.123 r_chiral_restr 0.105 r_ncsr_local_group_1 0.102 r_symmetry_nbtor_other 0.08 r_gen_planes_refined 0.017 r_bond_refined_d 0.014 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2913 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing