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Crystal structure of a Nitroreductase with bound FMN (Dhaf_2018) from Desulfitobacterium hafniense DCB-2 at 2.30 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 277 20.00% polyethylene glycol 3350, 0.20M ammonium dihydrogen phosphate, No Buffer pH 4.6, 0.001 M flavin mononucleotide (FMN), NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.39 48.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.261 α = 90 b = 81.577 β = 90 c = 161.754 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 CCD MARMOSAIC 325 mm CCD 2010-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.3 28.73 99.5 0.143 6.8 4.6 36709 36709 34.74
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.36 96.2 0.666 0.666 1.8 3.6 2593
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2.3 28.73 36660 1833 99.57 0.1773 0.1743 0.1857 0.2352 0.2393 RANDOM 51.0065
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] 0.01 0.34 -0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.413 r_dihedral_angle_3_deg 13.53 r_dihedral_angle_4_deg 11.811 r_scangle_it 6.693 r_scbond_it 4.666 r_dihedral_angle_1_deg 3.119 r_mcangle_it 2.626 r_angle_refined_deg 1.518 r_mcbond_it 1.417 r_angle_other_deg 0.949
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.413 r_dihedral_angle_3_deg 13.53 r_dihedral_angle_4_deg 11.811 r_scangle_it 6.693 r_scbond_it 4.666 r_dihedral_angle_1_deg 3.119 r_mcangle_it 2.626 r_angle_refined_deg 1.518 r_mcbond_it 1.417 r_angle_other_deg 0.949 r_mcbond_other 0.504 r_chiral_restr 0.088 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5694 Nucleic Acid Atoms Solvent Atoms 359 Heterogen Atoms 124
Software Software Software Name Purpose SHELX phasing REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction SHELXD phasing autoSHARP phasing