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New Irreversible a-l-Iduronidase Inhibitors and Activity-Based Probes
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3W81
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.1 M HEPES pH 7.5, 0.26 M Sodium potassium tartrate, 20 % w/v PEG3350
Crystal Properties Matthews coefficient Solvent content 2.38 48.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 206.86 α = 90 b = 69.89 β = 90 c = 93.69 γ = 90
Symmetry Space Group P 21 21 21
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 2018-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.02 66.21 94.4 0.164 0.184 0.08 0.986 5.4 4.9 84849
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.02 2.05 97.8 1.074 1.167 0.5 0.538 1.3 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 3w81 2.02 66.21 80558 4232 94.33 0.21433 0.21293 0.22 0.23985 0.2464 RANDOM 37.352
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] 1.24 0.11 -1.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.221 r_dihedral_angle_4_deg 15.656 r_dihedral_angle_3_deg 12.681 r_dihedral_angle_1_deg 6.477 r_long_range_B_refined 4.301 r_long_range_B_other 4.301 r_scangle_other 2.96 r_mcangle_it 2.58 r_mcangle_other 2.58 r_scbond_it 1.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.221 r_dihedral_angle_4_deg 15.656 r_dihedral_angle_3_deg 12.681 r_dihedral_angle_1_deg 6.477 r_long_range_B_refined 4.301 r_long_range_B_other 4.301 r_scangle_other 2.96 r_mcangle_it 2.58 r_mcangle_other 2.58 r_scbond_it 1.9 r_scbond_other 1.9 r_mcbond_it 1.722 r_mcbond_other 1.722 r_angle_refined_deg 1.263 r_angle_other_deg 0.753 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 9508 Nucleic Acid Atoms Solvent Atoms 243 Heterogen Atoms 190
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing