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Crystal structure of human lysosomal acid-alpha-glucosidase, GAA, in complex with iminosugar compound 4c
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NN3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 1.9 M AMMONIUM SULPHATE, 0.1 M HEPES,
REMARK 280 2% V/V PEG400, PH 7
Crystal Properties Matthews coefficient Solvent content 3.4 63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.372 α = 90 b = 102.298 β = 90 c = 128.155 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 EIGER X 16M 2018-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.978570 SOLEIL PROXIMA 1
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 1.8 48.23 99.9 0.091 0.099 0.039 0.998 11.3 6.6 117618 26.2
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 1.8 1.83 1.378 1.492 0.569 0.536 1.3 6.7
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 FOURIER SYNTHESIS FREE R-VALUE 1.8 48.23 111674 5855 99.84 0.16192 0.16038 0.1711 0.19168 0.2025 Taken over from parent data set 30.96
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] 0.98 -0.22 -0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.114 r_dihedral_angle_4_deg 16.356 r_dihedral_angle_3_deg 12.104 r_long_range_B_other 9.432 r_long_range_B_refined 9.412 r_scangle_other 9.337 r_scbond_it 7.434 r_scbond_other 7.433 r_dihedral_angle_1_deg 7.127 r_mcangle_it 4.502
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.114 r_dihedral_angle_4_deg 16.356 r_dihedral_angle_3_deg 12.104 r_long_range_B_other 9.432 r_long_range_B_refined 9.412 r_scangle_other 9.337 r_scbond_it 7.434 r_scbond_other 7.433 r_dihedral_angle_1_deg 7.127 r_mcangle_it 4.502 r_mcangle_other 4.502 r_mcbond_it 4.016 r_mcbond_other 4.009 r_angle_refined_deg 1.592 r_angle_other_deg 1.392 r_chiral_restr 0.082 r_gen_planes_refined 0.013 r_bond_refined_d 0.011 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 6631 Nucleic Acid Atoms Solvent Atoms 475 Heterogen Atoms 293
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction REFMAC phasing