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Crystal structure of Putative Flavoprotein in Complex with FMN (YP_213683.1) from Bacteroides fragilis NCTC 9343 at 1.75 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 10.0000% Glycerol, 1.2600M sodium citrate, 0.1M HEPES pH 7.5, Additive: 0.001 M FMN, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.06 59.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.764 α = 90 b = 96.764 β = 90 c = 47.882 γ = 90
Symmetry Space Group P 43 21 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 2009-05-13 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91162,0.97939,0.97927 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 1.75 27.832 99.2 0.057 17.33 23388 -3 22.346
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 1.75 1.81 94.2 0.732 1.9
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 1.75 27.832 23346 1196 99.76 0.15 0.148 0.1594 0.179 0.1889 RANDOM 29.843
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] -0.94 -0.94 1.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.974 r_dihedral_angle_4_deg 14.835 r_dihedral_angle_3_deg 12.388 r_dihedral_angle_1_deg 6.067 r_scangle_it 5.997 r_scbond_it 4.327 r_mcangle_it 2.803 r_mcbond_it 1.722 r_angle_refined_deg 1.548 r_angle_other_deg 0.961
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.974 r_dihedral_angle_4_deg 14.835 r_dihedral_angle_3_deg 12.388 r_dihedral_angle_1_deg 6.067 r_scangle_it 5.997 r_scbond_it 4.327 r_mcangle_it 2.803 r_mcbond_it 1.722 r_angle_refined_deg 1.548 r_angle_other_deg 0.961 r_mcbond_other 0.534 r_symmetry_vdw_refined 0.317 r_nbd_refined 0.217 r_nbd_other 0.201 r_symmetry_vdw_other 0.191 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.164 r_symmetry_hbond_refined 0.114 r_chiral_restr 0.101 r_metal_ion_refined 0.086 r_symmetry_metal_ion_refined 0.086 r_nbtor_other 0.083 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1258 Nucleic Acid Atoms Solvent Atoms 175 Heterogen Atoms 84
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