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Crystal structure of FMN-dependent nitroreductase BF3017 from Bacteroides fragilis NCTC 9343 (YP_212631.1) from Bacteroides fragilis NCTC 9343 at 1.55 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 277 0.2000M Li2SO4, 20.0000% PEG-1000, 0.1M Phosphate Citrate pH 4.2, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.39 48.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.873 α = 90 b = 48.873 β = 90 c = 295.194 γ = 120
Symmetry Space Group P 61 2 2
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 Flat collimating mirror, toroid focusing mirror 2009-03-18 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91162,0.97929,0.97905 SSRL BL9-2
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 1.55 29.514 99.5 0.08 15.72 13.59 31895 -3 20.36
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 1.55 1.61 98.6 0.016 1.6
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 MAD THROUGHOUT 1.55 29.514 31746 1599 99.52 0.162 0.161 0.1745 0.187 0.1985 RANDOM 25.523
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] 1.25 0.63 1.25 -1.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.339 r_dihedral_angle_4_deg 16.569 r_dihedral_angle_3_deg 15.697 r_scangle_it 7.933 r_scbond_it 5.859 r_dihedral_angle_1_deg 5.761 r_mcangle_it 2.963 r_mcbond_it 2.187 r_angle_refined_deg 1.705 r_angle_other_deg 1.027
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.339 r_dihedral_angle_4_deg 16.569 r_dihedral_angle_3_deg 15.697 r_scangle_it 7.933 r_scbond_it 5.859 r_dihedral_angle_1_deg 5.761 r_mcangle_it 2.963 r_mcbond_it 2.187 r_angle_refined_deg 1.705 r_angle_other_deg 1.027 r_mcbond_other 0.494 r_nbd_refined 0.239 r_symmetry_vdw_other 0.235 r_symmetry_hbond_refined 0.208 r_nbd_other 0.204 r_symmetry_vdw_refined 0.194 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.17 r_chiral_restr 0.105 r_nbtor_other 0.09 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1451 Nucleic Acid Atoms Solvent Atoms 207 Heterogen Atoms 65
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHELXD phasing autoSHARP phasing