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Crystal structure of a possible transglutaminase-family protein proteolytic fragment from Bacteroides fragilis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 294 100mM sodium cacodylate pH 6.5, 1.4M sodium acetate hydrate, Vapor diffusion, temperature 294K
Crystal Properties Matthews coefficient Solvent content 3.52 65.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.006 α = 90 b = 82.006 β = 90 c = 32.367 γ = 120
Symmetry Space Group P 31 2 1
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 MAR CCD 165 mm 2008-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97958 APS 31-ID
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 2.4 19.699 99.9 0.1 0.1 30.1 22 5084 5079 51.6
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) 2.4 2.53 99.8 0.574 0.574 5.8 22.3 737
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 2.4 15 5054 5050 224 99.92 0.226 0.225 0.2191 0.243 0.239 RANDOM 36.837
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] -1.07 -0.54 -1.07 1.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.687 r_dihedral_angle_3_deg 17.773 r_dihedral_angle_1_deg 6.364 r_scangle_it 3.122 r_scbond_it 2.016 r_mcangle_it 1.708 r_angle_refined_deg 1.527 r_mcbond_it 0.924 r_symmetry_vdw_refined 0.436 r_metal_ion_refined 0.325
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.687 r_dihedral_angle_3_deg 17.773 r_dihedral_angle_1_deg 6.364 r_scangle_it 3.122 r_scbond_it 2.016 r_mcangle_it 1.708 r_angle_refined_deg 1.527 r_mcbond_it 0.924 r_symmetry_vdw_refined 0.436 r_metal_ion_refined 0.325 r_symmetry_metal_ion_refined 0.32 r_nbtor_refined 0.307 r_nbd_refined 0.241 r_xyhbond_nbd_refined 0.137 r_chiral_restr 0.09 r_symmetry_hbond_refined 0.088 r_bond_refined_d 0.014 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 600 Nucleic Acid Atoms Solvent Atoms 5 Heterogen Atoms 1
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection MOSFLM data reduction SHELXCD phasing SHELXE model building