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Structure of Oxygen-Insensitive NAD(P)H-dependent Nitroreductase NfsB_Vv F70A/F108Y (NTR 2.0) in complex with FMN at 1.85 Angstroms resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DS7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291.15 Sodium acetate trihydrate pH 4.5, PEG 300
Crystal Properties Matthews coefficient Solvent content 2.61 52.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.43 α = 90 b = 137.36 β = 90 c = 107.04 γ = 90
Symmetry Space Group C 2 2 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 CCD ADSC QUANTUM 210r 2016-06-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.9537 Australian Synchrotron MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.85 68.68 99.9 0.12 18.3 14.4 43344
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.89 99.7 0.792 3.7 14.7
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 (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 1DS7 1.85 68.68 41147 2177 99.82 0.16628 0.16467 0.1762 0.19625 0.2025 RANDOM 17.826
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] 1.95 -1.27 -0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.469 r_dihedral_angle_4_deg 15.02 r_dihedral_angle_3_deg 12.962 r_dihedral_angle_1_deg 5.912 r_long_range_B_other 5.246 r_long_range_B_refined 5.245 r_scangle_other 4.343 r_scbond_it 2.934 r_scbond_other 2.933 r_mcangle_it 2.289
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.469 r_dihedral_angle_4_deg 15.02 r_dihedral_angle_3_deg 12.962 r_dihedral_angle_1_deg 5.912 r_long_range_B_other 5.246 r_long_range_B_refined 5.245 r_scangle_other 4.343 r_scbond_it 2.934 r_scbond_other 2.933 r_mcangle_it 2.289 r_mcangle_other 2.289 r_mcbond_it 1.712 r_angle_refined_deg 1.701 r_mcbond_other 1.659 r_angle_other_deg 1.494 r_chiral_restr 0.085 r_gen_planes_refined 0.013 r_bond_refined_d 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3346 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement Aimless data scaling MOSFLM data reduction PHASER phasing