8CB6

Crystal structure of human lysosomal acid-alpha-glucosidase, GAA, in covalent complex with TAMRA tagged 1,6-Epi-cylcophellitol aziridine activity based probe


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5NN3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72931.9 M AMMONIUM SULPHATE, 0.1 M HEPES, 2% V/V PEG400
Crystal Properties
Matthews coefficientSolvent content
3.3563

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.34α = 90
b = 102.945β = 90
c = 129.916γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2021-09-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 20.980112SOLEILPROXIMA 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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.948.671000.130.1350.0360.99914.513.7103337
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)RedundancyNumber Unique Reflections (All)
11.91.931001.6751.7390.4650.69513.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISFREE R-VALUE5NN31.948.6798106514699.950.150150.148710.17786RANDOM41.148
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]
0.780.02-0.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.023
r_dihedral_angle_4_deg16.506
r_dihedral_angle_3_deg11.977
r_dihedral_angle_1_deg7.04
r_long_range_B_refined6.937
r_long_range_B_other6.849
r_scangle_other6.263
r_scbond_it4.327
r_scbond_other4.326
r_mcangle_it3.321
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.023
r_dihedral_angle_4_deg16.506
r_dihedral_angle_3_deg11.977
r_dihedral_angle_1_deg7.04
r_long_range_B_refined6.937
r_long_range_B_other6.849
r_scangle_other6.263
r_scbond_it4.327
r_scbond_other4.326
r_mcangle_it3.321
r_mcangle_other3.321
r_mcbond_it2.671
r_mcbond_other2.666
r_angle_refined_deg1.572
r_angle_other_deg1.344
r_chiral_restr0.082
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms6691
Nucleic Acid Atoms
Solvent Atoms612
Heterogen Atoms281

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
REFMACphasing