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Crystal structure of Xylose Isomerase from an human intestinal tract microbe Bacteroides thetaiotaomicron
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 288 100 mM sodium chloride, 100 mM bicine pH9.0, 20%(v/v) polyethylene glycol monomethyl ether 550 (PEG MME
550)
Crystal Properties Matthews coefficient Solvent content 2.38 48.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.268 α = 82.76 b = 101.658 β = 68.24 c = 108.307 γ = 82.98
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 ADSC QUANTUM 270 2012-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.979350 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.1 50 98.3 19.4 3.9 214399
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 THROUGHOUT 2.1 38.21 188364 9914 90.58 0.18686 0.18558 0.1857 0.21131 0.2113 RANDOM 24.04
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] 0.09 -0.1 0.48 -0.13 -0.06 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.909 r_dihedral_angle_3_deg 11.935 r_dihedral_angle_4_deg 11.4 r_dihedral_angle_1_deg 4.342 r_long_range_B_refined 2.734 r_angle_refined_deg 0.786 r_mcangle_it 0.485 r_mcbond_it 0.265 r_scbond_it 0.234 r_chiral_restr 0.056
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.909 r_dihedral_angle_3_deg 11.935 r_dihedral_angle_4_deg 11.4 r_dihedral_angle_1_deg 4.342 r_long_range_B_refined 2.734 r_angle_refined_deg 0.786 r_mcangle_it 0.485 r_mcbond_it 0.265 r_scbond_it 0.234 r_chiral_restr 0.056 r_bond_refined_d 0.004 r_gen_planes_refined 0.002 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 27384 Nucleic Acid Atoms Solvent Atoms 2600 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement PHENIX phasing HKL-2000 data scaling