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Structure of the two subsite D-xylosidase from Selenomonas ruminantium in complex with 1,3-bis[tris(hydroxymethyl)methylamino]propane
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 4 L of protein solution (1.6 mg/mL in 0.1 M BTP-HCl pH 8.0) mixed with 1 L of the well solution containing 22-25% (w/v) PEG 1100 monomethyl ether in 0.1M BTP-HCl, pH 8.0., VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.25 45.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.579 α = 67.84 b = 84.401 β = 81.31 c = 94.039 γ = 75.08
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 225 mm CCD 2005-07-19 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 5ID-B 0.9784, 0.9786, 0.9632 APS 5ID-B
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 1.2 100 94.5 0.063 12.55 4.48 667241 630354 -3 17.2
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 1.24 91.4 0.382 3.65 3.89 57143
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 1.3 87.04 474622 24998 95.29 0.13572 0.13427 0.1471 0.16303 0.1745 RANDOM 11.81
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] -0.46 1.1 -0.41 -0.11 0.12 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.865 r_dihedral_angle_4_deg 17.043 r_dihedral_angle_3_deg 11.777 r_sphericity_free 9.143 r_dihedral_angle_1_deg 6.787 r_sphericity_bonded 4.398 r_scangle_it 3.675 r_scbond_it 2.965 r_mcangle_it 2.079 r_mcbond_it 1.758
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.865 r_dihedral_angle_4_deg 17.043 r_dihedral_angle_3_deg 11.777 r_sphericity_free 9.143 r_dihedral_angle_1_deg 6.787 r_sphericity_bonded 4.398 r_scangle_it 3.675 r_scbond_it 2.965 r_mcangle_it 2.079 r_mcbond_it 1.758 r_angle_refined_deg 1.656 r_rigid_bond_restr 1.504 r_angle_other_deg 1.091 r_mcbond_other 0.849 r_symmetry_vdw_other 0.246 r_nbd_refined 0.2 r_nbd_other 0.193 r_nbtor_refined 0.187 r_symmetry_hbond_refined 0.166 r_xyhbond_nbd_refined 0.142 r_symmetry_vdw_refined 0.112 r_chiral_restr 0.11 r_nbtor_other 0.088 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17832 Nucleic Acid Atoms Solvent Atoms 2050 Heterogen Atoms 81
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data reduction XDS data scaling XSCALE data scaling SnB phasing