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Crystal structure of a Michaelis complex of alpha-L-fucosidase GH29 from Bacteroides thetaiotaomicron with the synthetic substrate 4- nitrophenyl-alpha-L-fucose
Crystallization Crystal Properties Matthews coefficient Solvent content 2.4 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.61 α = 90 b = 184.82 β = 94.63 c = 98.06 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 CCD ADSC CCD 2009-05-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 1.95 50 98.4 0.1 9.2 3.5 138108 2
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 MOLECULAR REPLACEMENT THROUGHOUT 1.95 47.25 131113 6950 98.34 0.18115 0.17862 0.22889 0.223 RANDOM 21.362
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 -0.34 1.39 -1.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.279 r_dihedral_angle_4_deg 22.574 r_dihedral_angle_3_deg 16.017 r_dihedral_angle_1_deg 5.894 r_scangle_it 3.385 r_scbond_it 2.136 r_angle_refined_deg 1.344 r_mcangle_it 1.288 r_mcbond_it 0.71 r_chiral_restr 0.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.279 r_dihedral_angle_4_deg 22.574 r_dihedral_angle_3_deg 16.017 r_dihedral_angle_1_deg 5.894 r_scangle_it 3.385 r_scbond_it 2.136 r_angle_refined_deg 1.344 r_mcangle_it 1.288 r_mcbond_it 0.71 r_chiral_restr 0.097 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 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_other r_long_range_B_refined 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 14248 Nucleic Acid Atoms Solvent Atoms 1394 Heterogen Atoms 115
Software Software Software Name Purpose REFMAC refinement