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Crystal structure of putative oxidoreductase (YP_213212.1) from Bacteroides fragilis NCTC 9343 at 1.99 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 10.0000% iso-Propanol, 20.0000% PEG-4000, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.5 50.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.37 α = 90 b = 80.82 β = 90 c = 101.47 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) 2008-08-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 SSRL BL11-1
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 1.99 28.76 96.8 0.107 7.12 4.84 39369 -3 23.863
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 2.01 2.08 84.7 0.657 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 SAD THROUGHOUT 1.99 28.76 39318 1974 99.31 0.171 0.169 0.1743 0.224 0.2216 RANDOM 27.7
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] 3.67 -1.59 -2.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.15 r_dihedral_angle_3_deg 13.138 r_dihedral_angle_4_deg 11.9 r_scangle_it 7.282 r_scbond_it 5.687 r_dihedral_angle_1_deg 3.737 r_mcangle_it 2.941 r_mcbond_it 2.211 r_angle_refined_deg 1.66 r_angle_other_deg 0.989
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.15 r_dihedral_angle_3_deg 13.138 r_dihedral_angle_4_deg 11.9 r_scangle_it 7.282 r_scbond_it 5.687 r_dihedral_angle_1_deg 3.737 r_mcangle_it 2.941 r_mcbond_it 2.211 r_angle_refined_deg 1.66 r_angle_other_deg 0.989 r_mcbond_other 0.584 r_symmetry_vdw_other 0.249 r_nbd_refined 0.208 r_nbd_other 0.205 r_symmetry_hbond_refined 0.19 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.162 r_chiral_restr 0.098 r_nbtor_other 0.089 r_symmetry_vdw_refined 0.078 r_bond_refined_d 0.018 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3972 Nucleic Acid Atoms Solvent Atoms 364 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHARP phasing