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Crystal structure of human alpha-galactosidase A in complex with alpha-galactose configured cyclosulfate ME776
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 2.8 56.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.34 α = 90 b = 90.34 β = 90 c = 216 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 PILATUS 6M-F 2018-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97951 Diamond I04
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 2.07 78.36 100 0.124 0.052 0.998 9.8 12.2 63220
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.07 2.12 0.745 1
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 2.07 78.36 60057 3072 99.94 0.18298 0.18007 0.1862 0.2416 0.2399 RANDOM 55.243
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] 1.64 0.82 1.64 -5.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.049 r_dihedral_angle_4_deg 16.481 r_dihedral_angle_3_deg 14.98 r_long_range_B_refined 7.909 r_long_range_B_other 7.908 r_dihedral_angle_1_deg 7.501 r_scangle_other 6.646 r_mcangle_it 5.105 r_mcangle_other 5.105 r_scbond_it 4.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.049 r_dihedral_angle_4_deg 16.481 r_dihedral_angle_3_deg 14.98 r_long_range_B_refined 7.909 r_long_range_B_other 7.908 r_dihedral_angle_1_deg 7.501 r_scangle_other 6.646 r_mcangle_it 5.105 r_mcangle_other 5.105 r_scbond_it 4.86 r_scbond_other 4.859 r_mcbond_it 3.897 r_mcbond_other 3.893 r_angle_refined_deg 1.568 r_angle_other_deg 1.296 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 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 6242 Nucleic Acid Atoms Solvent Atoms 272 Heterogen Atoms 409
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing