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Crystal structure of the C-terminal domain of uncharacterized protein from Bacteroides fragilis NCTC 9343
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 0.2 M Potassium sodium tartrate tetrahydrate
20% Peg 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.19 43.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.145 α = 90 b = 43.428 β = 90 c = 98.692 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 SBC-3 mirror 2008-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.9794 APS 19-BM
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 1.3 50 91.2 0.043 44.7 8 35647 32763 2 2
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 1.3 1.334 50 0.15 5.14 4 884
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1.3 49.33 2 2 32675 31061 1646 91.09 0.14032 0.14032 0.13872 0.1398 0.17009 0.1704 RANDOM 12.084
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] 0.17 0.29 -0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.543 r_dihedral_angle_4_deg 14.41 r_dihedral_angle_3_deg 12.804 r_sphericity_free 10.178 r_dihedral_angle_1_deg 6.242 r_scangle_it 5.331 r_sphericity_bonded 4.678 r_scbond_it 3.709 r_mcangle_it 2.858 r_mcbond_it 1.856
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.543 r_dihedral_angle_4_deg 14.41 r_dihedral_angle_3_deg 12.804 r_sphericity_free 10.178 r_dihedral_angle_1_deg 6.242 r_scangle_it 5.331 r_sphericity_bonded 4.678 r_scbond_it 3.709 r_mcangle_it 2.858 r_mcbond_it 1.856 r_angle_refined_deg 1.711 r_rigid_bond_restr 1.65 r_angle_other_deg 1.019 r_mcbond_other 0.869 r_chiral_restr 0.12 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1128 Nucleic Acid Atoms Solvent Atoms 230 Heterogen Atoms
Software Software Software Name Purpose SBC-Collect data collection HKL-3000 phasing SHELX model building Coot model building MLPHARE phasing PHENIX model building REFMAC refinement ARP/wARP model building HKL-3000 data reduction HKL-3000 data scaling SHELX phasing PHENIX phasing REFMAC phasing