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Crystal structure of putative glycosyl hydrolase, was Domain of Unknown Function (DUF1080) (YP_001302580.1) from Parabacteroides distasonis ATCC 8503 at 2.36 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 0.2000M Li2SO4, 30.0000% PEG-4000, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.86 56.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.009 α = 90 b = 61.009 β = 90 c = 167.332 γ = 90
Symmetry Space Group P 41 21 2
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 collimating mirror, toroid focusing mirror 2009-03-19 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91837,0.97932,0.97915 SSRL BL9-2
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 2.36 29.336 99.1 0.069 13.77 13756 -3 60.809
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 2.36 2.44 92.8 0.951 1.4
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 MAD THROUGHOUT 2.36 29.336 13695 685 99.71 0.2 0.198 0.1977 0.245 0.2467 RANDOM 50.313
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] -0.21 -0.21 0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.272 r_dihedral_angle_3_deg 10.911 r_dihedral_angle_4_deg 10.164 r_scangle_it 5.131 r_scbond_it 4.258 r_dihedral_angle_1_deg 3.86 r_mcangle_it 2.384 r_angle_refined_deg 1.651 r_mcbond_it 1.479 r_angle_other_deg 0.994
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.272 r_dihedral_angle_3_deg 10.911 r_dihedral_angle_4_deg 10.164 r_scangle_it 5.131 r_scbond_it 4.258 r_dihedral_angle_1_deg 3.86 r_mcangle_it 2.384 r_angle_refined_deg 1.651 r_mcbond_it 1.479 r_angle_other_deg 0.994 r_mcbond_other 0.274 r_symmetry_hbond_refined 0.218 r_xyhbond_nbd_refined 0.197 r_symmetry_vdw_refined 0.192 r_nbd_other 0.177 r_nbtor_refined 0.176 r_nbd_refined 0.175 r_symmetry_vdw_other 0.134 r_chiral_restr 0.099 r_nbtor_other 0.088 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1781 Nucleic Acid Atoms Solvent Atoms 77 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHELXD phasing autoSHARP phasing