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Crystal structure of human lysosomal acid-alpha-glucosidase, GAA, in complex with cyclosulfamidate 4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NN4
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 PH 7.0, 2% V/V PEG400
Crystal Properties Matthews coefficient Solvent content 3.4 63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.157 α = 90 b = 102.539 β = 90 c = 129.048 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 2019-09-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.9801 SOLEIL PROXIMA 2
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 1.85 47.65 100 0.121 0.13 0.049 0.998 14.5 13.6 110461 20.85
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.88 99.9 1.554 0.628 0.742 2.1
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 (All) 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 5nn4 1.85 47 110373 5503 99.952 0.15 0.14978 0.1485 0.1618 0.1753 0.1891 taken over form entry 5NN4 28.703
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] 1.237 -0.8 -0.437
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.274 r_dihedral_angle_4_deg 15.751 r_scbond_it 12.111 r_scbond_other 12.11 r_dihedral_angle_3_deg 11.954 r_scangle_it 11.857 r_scangle_other 11.856 r_lrange_other 10.882 r_lrange_it 10.829 r_dihedral_angle_1_deg 6.846
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.274 r_dihedral_angle_4_deg 15.751 r_scbond_it 12.111 r_scbond_other 12.11 r_dihedral_angle_3_deg 11.954 r_scangle_it 11.857 r_scangle_other 11.856 r_lrange_other 10.882 r_lrange_it 10.829 r_dihedral_angle_1_deg 6.846 r_mcangle_it 4.97 r_mcangle_other 4.969 r_mcbond_it 4.642 r_mcbond_other 4.641 r_angle_refined_deg 1.513 r_angle_other_deg 1.355 r_nbd_other 0.242 r_nbd_refined 0.194 r_symmetry_nbd_other 0.184 r_xyhbond_nbd_refined 0.179 r_nbtor_refined 0.17 r_symmetry_xyhbond_nbd_refined 0.161 r_symmetry_nbd_refined 0.147 r_symmetry_xyhbond_nbd_other 0.092 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6691 Nucleic Acid Atoms Solvent Atoms 778 Heterogen Atoms 265
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing