8CB1

Crystal structure of human lysosomal acid-alpha-glucosidase, GAA, in complex with N-PNT-DNM 15


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
3.462.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.75α = 90
b = 102.604β = 90
c = 129.179γ = 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 20.98011SOLEILPROXIMA 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
11.7548.381000.120.1240.0310.99914.115.6129900
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)
11.751.782.0652.1350.5370.57315

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 SYNTHESISTHROUGHOUT5NN31.7547.73123307650199.960.143840.142240.1749RANDOM40.587
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]
0.070.06-0.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.751
r_dihedral_angle_4_deg15.823
r_dihedral_angle_3_deg11.926
r_long_range_B_refined8.2
r_long_range_B_other8.17
r_scangle_other7.9
r_dihedral_angle_1_deg7.054
r_scbond_it6.017
r_scbond_other6.017
r_mcangle_it3.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.751
r_dihedral_angle_4_deg15.823
r_dihedral_angle_3_deg11.926
r_long_range_B_refined8.2
r_long_range_B_other8.17
r_scangle_other7.9
r_dihedral_angle_1_deg7.054
r_scbond_it6.017
r_scbond_other6.017
r_mcangle_it3.86
r_mcangle_other3.86
r_mcbond_it3.422
r_mcbond_other3.42
r_angle_refined_deg1.619
r_angle_other_deg1.418
r_chiral_restr0.085
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_bond_other_d0.002
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 Atoms6661
Nucleic Acid Atoms
Solvent Atoms785
Heterogen Atoms312

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
REFMACphasing