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Crystal structure of Nitroreductase with Bound FMN (YP_211706.1) from Bacteroides fragilis NCTC 9343 at 1.70 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 277 65.0000% MPD, 0.1M TRIS pH 8.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2.33 47.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.61 α = 90 b = 83.73 β = 90 c = 116.51 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 MARMOSAIC 325 mm CCD Flat collimating mirror, toroid focusing mirror 2008-08-04 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91162,0.97932,0.97918 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 29.123 96.3 0.058 0.08 10.63 21975 -3 17.497
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.76 94.4 0.521 0.715 1.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 1.7 29.123 21941 1124 98.47 0.152 0.15 0.183 0.1767 RANDOM 17.359
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] -1.39 2.35 -0.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.756 r_dihedral_angle_4_deg 14.226 r_dihedral_angle_3_deg 12.202 r_dihedral_angle_1_deg 5.394 r_scangle_it 5.061 r_scbond_it 3.881 r_mcangle_it 2.204 r_mcbond_it 1.803 r_angle_refined_deg 1.367 r_angle_other_deg 0.926
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.756 r_dihedral_angle_4_deg 14.226 r_dihedral_angle_3_deg 12.202 r_dihedral_angle_1_deg 5.394 r_scangle_it 5.061 r_scbond_it 3.881 r_mcangle_it 2.204 r_mcbond_it 1.803 r_angle_refined_deg 1.367 r_angle_other_deg 0.926 r_mcbond_other 0.477 r_xyhbond_nbd_refined 0.252 r_nbd_refined 0.227 r_nbd_other 0.191 r_nbtor_refined 0.185 r_symmetry_vdw_other 0.177 r_symmetry_vdw_refined 0.168 r_symmetry_hbond_refined 0.139 r_nbtor_other 0.085 r_chiral_restr 0.083 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1437 Nucleic Acid Atoms Solvent Atoms 205 Heterogen Atoms 63
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