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Crystal structure of putative phosphosugar isomerase involved in capsule formation (YP_209877.1) from Bacteroides fragilis NCTC 9343 at 1.70 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 277 5.0% PEG-6000, 0.1M MES pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.04 39.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.409 α = 90 b = 114.267 β = 90 c = 115.917 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 Flat mirror (vertical focusing) 2008-08-01 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837,0.97910,0.97849 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.7 29.223 99.8 0.103 0.103 5.554 4.5 88793 19.097
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 1.7 1.74 100 0.819 0.819 0.9 4.5 6471
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 1.7 29.223 88524 4437 99.56 0.173 0.172 0.1792 0.197 0.2026 RANDOM 18.583
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] -1.15 -0.22 1.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.345 r_dihedral_angle_4_deg 16.063 r_dihedral_angle_3_deg 12.78 r_scangle_it 6.256 r_dihedral_angle_1_deg 5.034 r_scbond_it 3.889 r_mcangle_it 2.044 r_angle_refined_deg 1.446 r_mcbond_it 1.114 r_angle_other_deg 0.977
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.345 r_dihedral_angle_4_deg 16.063 r_dihedral_angle_3_deg 12.78 r_scangle_it 6.256 r_dihedral_angle_1_deg 5.034 r_scbond_it 3.889 r_mcangle_it 2.044 r_angle_refined_deg 1.446 r_mcbond_it 1.114 r_angle_other_deg 0.977 r_mcbond_other 0.255 r_chiral_restr 0.088 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5871 Nucleic Acid Atoms Solvent Atoms 725 Heterogen Atoms 180
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction SHELXD phasing autoSHARP phasing