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Structure of Ddn, the Deazaflavin-dependent nitroreductase from Mycobacterium tuberculosis involved in bioreductive activation of PA-824, with co-factor F420
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3R5P PDB entry 3R5P (preliminary model)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 0.1 M HEPES, 1.4 M tri-Na-citrate with equimolar protein and F420, pH 7.5, vapor diffusion, sitting drop, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.98 69.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 146.947 α = 90 b = 91.715 β = 119.53 c = 86.499 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 CCD ADSC QUANTUM 315r 2009-07-10 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 315r 2009-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 0.979 ALS 5.0.2 2 SYNCHROTRON ALS BEAMLINE 5.0.2 0.979 ALS 5.0.2
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 1,2 2.1 50 97.9 0.112 10.7 2.4 56945 56945
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) 1,2 2.1 2.18 98.1 0.473 1.892 2.5 5696
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 PDB entry 3R5P (preliminary model) 2.101 46.674 0.11 53846 53828 2724 92.42 0.2285 0.2267 0.2282 0.2631 0.2597 random 22.939
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] -0.2614 2.0418 -0.4141 0.6755
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 20.186 f_angle_d 1.039 f_chiral_restr 0.064 f_bond_d 0.006 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4370 Nucleic Acid Atoms Solvent Atoms 438 Heterogen Atoms 265
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction BOS data collection HKL-2000 data reduction HKL-2000 data scaling