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Crystal structure of the C-terminal domain of a chitobiase (BF3579) from Bacteroides fragilis, Northeast Structural Genomics Consortium Target BfR260B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 microbatch under oil 5 277 Protein solution: 10 mM Tris (pH 7.5), 100 mM sodium chloride, and 5 mM DTT. Reservoir solution: 100 mM NaAcetate (pH 5), 40% PEG 8K, and 100 mM NH4Cl , microbatch under oil, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.21 44.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.893 α = 90 b = 51.684 β = 90 c = 63.96 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 ADSC QUANTUM 4 mirrors 2008-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A NSLS X4A
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 1.3 30 89.2 0.039 0.044 43.3 5 75798 67612 2 2 9.1
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 1.3 1.35 72.1 0.081 0.089 11.54 2.9 7565
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 10 2 2 35268 35268 1854 100 0.15628 0.15618 0.1552 0.1665 0.17455 0.1815 RANDOM 12.287
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] -0.23 0.38 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.752 r_dihedral_angle_4_deg 16.307 r_dihedral_angle_3_deg 9.438 r_dihedral_angle_1_deg 7.08 r_scangle_it 2.01 r_sphericity_free 1.864 r_sphericity_bonded 1.484 r_scbond_it 1.424 r_angle_refined_deg 1.068 r_mcangle_it 0.987
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.752 r_dihedral_angle_4_deg 16.307 r_dihedral_angle_3_deg 9.438 r_dihedral_angle_1_deg 7.08 r_scangle_it 2.01 r_sphericity_free 1.864 r_sphericity_bonded 1.484 r_scbond_it 1.424 r_angle_refined_deg 1.068 r_mcangle_it 0.987 r_rigid_bond_restr 0.833 r_mcbond_it 0.655 r_nbtor_refined 0.303 r_nbd_refined 0.179 r_symmetry_vdw_refined 0.121 r_xyhbond_nbd_refined 0.096 r_chiral_restr 0.074 r_symmetry_hbond_refined 0.059 r_bond_refined_d 0.006 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1168 Nucleic Acid Atoms Solvent Atoms 386 Heterogen Atoms
Software Software Software Name Purpose ADSC data collection SOLVE phasing RESOLVE model building CNS refinement HKL-2000 data reduction SCALEPACK data scaling RESOLVE phasing