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Crystal structure of human lysosomal acid-alpha-glucosidase, GAA, in complex with iminosugar compound 4d
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 = 97.032 α = 90 b = 102.723 β = 90 c = 129.317 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 9M 2021-06-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.976254 ESRF ID30B
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 1.95 47.71 100 0.23 0.257 0.112 0.985 5.2 5.2 94745 17.8
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 1.95 1.98 1.286 1.445 0.651 0.539 1.1 4.9
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 1.95 47.71 89894 4741 99.9 0.16928 0.16733 0.1734 0.20682 0.2114 Taken over from parent data set 38.782
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] 1.12 0.09 -1.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.594 r_dihedral_angle_4_deg 17.982 r_dihedral_angle_3_deg 12.858 r_dihedral_angle_1_deg 7.384 r_long_range_B_refined 6.999 r_long_range_B_other 6.866 r_scangle_other 6.074 r_scbond_it 4.369 r_scbond_other 4.369 r_mcangle_it 3.586
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.594 r_dihedral_angle_4_deg 17.982 r_dihedral_angle_3_deg 12.858 r_dihedral_angle_1_deg 7.384 r_long_range_B_refined 6.999 r_long_range_B_other 6.866 r_scangle_other 6.074 r_scbond_it 4.369 r_scbond_other 4.369 r_mcangle_it 3.586 r_mcangle_other 3.586 r_mcbond_it 2.908 r_mcbond_other 2.903 r_angle_refined_deg 1.431 r_angle_other_deg 1.267 r_chiral_restr 0.069 r_gen_planes_refined 0.011 r_bond_refined_d 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 6668 Nucleic Acid Atoms Solvent Atoms 786 Heterogen Atoms 318
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction REFMAC phasing