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The bacterial orthologue of Human a-L-iduronidase does not need N-glycan post-translational modifications to be catalytically competent: Crystallography and QM/MM insights into Mucopolysaccharidosis I
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other See our manuscript for the template
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 1 M succinic acid, 1% PEG 2000 MME and 100 mM HEPES pH 7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 173.028 α = 90 b = 173.028 β = 90 c = 156.687 γ = 120
Symmetry Space Group P 62 2 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 PIXEL DECTRIS PILATUS3 S 6M 2014-12-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.2 20 99.9 0.061 0.013 38.9 22.2 70222
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.32 100 0.64 0.137 5.6 22.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT See our manuscript for the template 2.2 149.85 68241 1939 99.81 0.15913 0.15865 0.1681 0.17499 0.1843 RANDOM 46.533
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] -1.05 -0.53 -1.05 3.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.122 r_dihedral_angle_4_deg 20.373 r_dihedral_angle_3_deg 14.496 r_long_range_B_refined 8.528 r_long_range_B_other 8.528 r_dihedral_angle_1_deg 7.35 r_scangle_other 4.79 r_mcangle_it 3.76 r_mcangle_other 3.76 r_scbond_it 3.071
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.122 r_dihedral_angle_4_deg 20.373 r_dihedral_angle_3_deg 14.496 r_long_range_B_refined 8.528 r_long_range_B_other 8.528 r_dihedral_angle_1_deg 7.35 r_scangle_other 4.79 r_mcangle_it 3.76 r_mcangle_other 3.76 r_scbond_it 3.071 r_scbond_other 3.071 r_mcbond_it 2.372 r_mcbond_other 2.366 r_angle_refined_deg 1.908 r_angle_other_deg 1.08 r_chiral_restr 0.115 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4721 Nucleic Acid Atoms Solvent Atoms 384 Heterogen Atoms 105
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing