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Crystal structure of alpha-galactosidase A at pH 4.5 complexed with 1-deoxygalactonijirimycin
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION vapor diffusion
Crystal Properties Matthews coefficient Solvent content 2.77 55.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.61 α = 90 b = 89.61 β = 90 c = 216.64 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.7 77.6 27633
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 2.7 19.9 26233 1400 97.29 0.24509 0.24193 0.2385 0.30577 0.301 RANDOM 57.738
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] -0.14 -0.07 -0.14 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.935 r_dihedral_angle_3_deg 21.561 r_dihedral_angle_4_deg 18.923 r_dihedral_angle_1_deg 9.413 r_angle_refined_deg 1.95 r_scangle_it 1.775 r_scbond_it 1.207 r_mcangle_it 0.668 r_mcbond_it 0.412 r_symmetry_vdw_refined 0.349
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.935 r_dihedral_angle_3_deg 21.561 r_dihedral_angle_4_deg 18.923 r_dihedral_angle_1_deg 9.413 r_angle_refined_deg 1.95 r_scangle_it 1.775 r_scbond_it 1.207 r_mcangle_it 0.668 r_mcbond_it 0.412 r_symmetry_vdw_refined 0.349 r_nbtor_refined 0.331 r_nbd_refined 0.262 r_xyhbond_nbd_refined 0.208 r_symmetry_hbond_refined 0.2 r_chiral_restr 0.127 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6253 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 256
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction XSCALE data scaling