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Crystal structure of a putative glycoside hydrolase (BDI_3141) from Parabacteroides distasonis ATCC 8503 at 1.70 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 20% polyethylene glycol 3350, 0.2M magnesium acetate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.31 46.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.361 α = 90 b = 56.361 β = 90 c = 231.759 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 Vertical focusing mirror; double crystal Si(111) monochromator 2011-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL14-1 SSRL BL14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.7 28.97 100 0.124 14.4 14.2 42521 42521 17.622
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 1.7 1.74 100 0.892 0.892 0.9 12.9 3047
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 SAD THROUGHOUT 1.7 28.97 42405 2138 99.96 0.1502 0.149 0.1608 0.1718 0.1813 RANDOM 19.109
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] -0.33 -0.33 0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.533 r_dihedral_angle_4_deg 12.256 r_dihedral_angle_3_deg 11.95 r_dihedral_angle_1_deg 6.867 r_angle_refined_deg 1.386 r_angle_other_deg 0.863 r_chiral_restr 0.086 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.533 r_dihedral_angle_4_deg 12.256 r_dihedral_angle_3_deg 11.95 r_dihedral_angle_1_deg 6.867 r_angle_refined_deg 1.386 r_angle_other_deg 0.863 r_chiral_restr 0.086 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2753 Nucleic Acid Atoms Solvent Atoms 327 Heterogen Atoms 69
Software Software Software Name Purpose MolProbity model building PDB_EXTRACT data extraction SHELX phasing SHARP phasing SCALA data scaling REFMAC refinement MOSFLM data reduction SHELXD phasing