☰ Navigation Tabs
Crystal structure of human lysosomal acid-alpha-glucosidase, GAA, in complex with N-acetyl-cysteine
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 pH 7.0, 2% v/v PEG400
Crystal Properties Matthews coefficient Solvent content 3.39 63.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.435 α = 90 b = 102.303 β = 90 c = 129.068 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 PILATUS3 6M 2014-07-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.95373 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.83 47.66 99.6 0.072 0.04 0.999 17.8 7.5 113752 21.25
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 1.83 1.86 92 0.569 0.311 0.859 3.3 7.1
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 (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 THROUGHOUT 5NN3 1.83 47.66 107574 5639 99.25 0.15487 0.15366 0.1658 0.17827 0.1911 RANDOM 26.421
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] 0.92 -0.13 -0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.914 r_dihedral_angle_4_deg 15.28 r_dihedral_angle_3_deg 12.056 r_dihedral_angle_1_deg 6.365 r_angle_refined_deg 1.327 r_angle_other_deg 0.742 r_chiral_restr 0.077 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.914 r_dihedral_angle_4_deg 15.28 r_dihedral_angle_3_deg 12.056 r_dihedral_angle_1_deg 6.365 r_angle_refined_deg 1.327 r_angle_other_deg 0.742 r_chiral_restr 0.077 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6667 Nucleic Acid Atoms Solvent Atoms 776 Heterogen Atoms 329
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing