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Crystal structure of human alpha-galactosidase A in complex with alpha-galactose configured cyclophellitol aziridine ME737
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 2.81 56.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.39 α = 90 b = 90.39 β = 90 c = 216.59 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 2018-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.915870 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.04 63.52 100 0.068 0.986 5.6 12.3 66254
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 2.04 2.09 0.81 0.8
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 2.04 63.52 62943 3204 99.89 0.19811 0.19504 0.1999 0.26001 0.2598 RANDOM 54.268
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] 1.82 0.91 1.82 -5.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.414 r_dihedral_angle_3_deg 15.983 r_dihedral_angle_4_deg 15.054 r_long_range_B_refined 7.692 r_long_range_B_other 7.692 r_dihedral_angle_1_deg 7.652 r_scangle_other 6.276 r_mcangle_it 4.879 r_mcangle_other 4.879 r_scbond_it 4.461
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.414 r_dihedral_angle_3_deg 15.983 r_dihedral_angle_4_deg 15.054 r_long_range_B_refined 7.692 r_long_range_B_other 7.692 r_dihedral_angle_1_deg 7.652 r_scangle_other 6.276 r_mcangle_it 4.879 r_mcangle_other 4.879 r_scbond_it 4.461 r_scbond_other 4.46 r_mcbond_it 3.659 r_mcbond_other 3.648 r_angle_refined_deg 1.53 r_angle_other_deg 1.263 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 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 6242 Nucleic Acid Atoms Solvent Atoms 240 Heterogen Atoms 317
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing