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Crystal structure of human alpha-galactosidase A in complex with alpha-galactose configured cyclosulfamidate ME763
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R46
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 PEG 4000 (50%), sodium acetate (pH 4.6) and lithium sulfate,
Crystal Properties Matthews coefficient Solvent content 2.82 56.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.57 α = 90 b = 90.57 β = 90 c = 216.46 γ = 120
Symmetry Space Group P 32 2 1
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 6M 2018-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.99 63.59 100 0.109 0.032 0.999 11.5 12.2 71557
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.99 2.03 0.987 0.732
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 1r46 1.99 63.59 67934 3498 99.89 0.18757 0.18477 0.1948 0.24394 0.2477 RANDOM 56.986
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] 1.72 0.86 1.72 -5.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.11 r_dihedral_angle_4_deg 18.58 r_dihedral_angle_3_deg 15.05 r_long_range_B_refined 8.242 r_long_range_B_other 8.242 r_dihedral_angle_1_deg 7.692 r_scangle_other 6.995 r_mcangle_it 5.17 r_mcangle_other 5.17 r_scbond_it 5.144
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.11 r_dihedral_angle_4_deg 18.58 r_dihedral_angle_3_deg 15.05 r_long_range_B_refined 8.242 r_long_range_B_other 8.242 r_dihedral_angle_1_deg 7.692 r_scangle_other 6.995 r_mcangle_it 5.17 r_mcangle_other 5.17 r_scbond_it 5.144 r_scbond_other 5.144 r_mcbond_it 4.022 r_mcbond_other 4.018 r_angle_refined_deg 1.582 r_angle_other_deg 1.3 r_chiral_restr 0.072 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 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 6245 Nucleic Acid Atoms Solvent Atoms 274 Heterogen Atoms 402
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing