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Crystal structure of a susD homolog (BT1281) from Bacteroides thetaiotaomicron VPI-5482 at 1.90 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 0.2000M magnesium acetate, 20.0000% polyethylene glycol 8000, 0.1M sodium cacodylate pH 6.5, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.37 48.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.146 α = 78.73 b = 74.673 β = 73.51 c = 78.057 γ = 78.62
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator 2013-07-16 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.9794,0.9184,0.9793 SSRL BL12-2
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 1.9 28.387 84.9 0.075 5.07 2.4 74269 -3 23.939
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 1.9 1.97 74.6 0.239 1.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 1.9 28.387 74269 3702 87.63 0.1369 0.1348 0.1757 0.1798 RANDOM 25.2532
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] -0.73 -0.14 0.58 1.38 -0.39 -0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.69 r_dihedral_angle_4_deg 16.68 r_dihedral_angle_3_deg 12.173 r_dihedral_angle_1_deg 5.911 r_mcangle_it 3.065 r_mcbond_it 2.372 r_mcbond_other 2.369 r_angle_refined_deg 1.517 r_angle_other_deg 0.962 r_chiral_restr 0.049
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.69 r_dihedral_angle_4_deg 16.68 r_dihedral_angle_3_deg 12.173 r_dihedral_angle_1_deg 5.911 r_mcangle_it 3.065 r_mcbond_it 2.372 r_mcbond_other 2.369 r_angle_refined_deg 1.517 r_angle_other_deg 0.962 r_chiral_restr 0.049 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.004 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7566 Nucleic Acid Atoms Solvent Atoms 859 Heterogen Atoms 70
Software Software Software Name Purpose MolProbity model building PDB_EXTRACT data extraction SHELX phasing SHARP phasing XSCALE data scaling REFMAC refinement XDS data reduction SHELXD phasing autoSHARP phasing