9GSW | pdb_00009gsw

Crystal structure of human lysosomal acid-alpha-glucosidase, GAA, in complex with iminosugar compound 4d


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, REMARK 280 2% V/V PEG400, PH 7
Crystal Properties
Matthews coefficientSolvent content
3.463

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.032α = 90
b = 102.723β = 90
c = 129.317γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2021-06-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID30B0.976254ESRFID30B

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
11.9547.711000.230.2570.1120.9855.25.29474517.8
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)RedundancyNumber Unique Reflections (All)
11.951.981.2861.4450.6510.5391.14.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISFREE R-VALUE1.9547.7189894474199.90.169280.167330.17340.206820.2114Taken over from parent data set38.782
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]
1.120.09-1.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.594
r_dihedral_angle_4_deg17.982
r_dihedral_angle_3_deg12.858
r_dihedral_angle_1_deg7.384
r_long_range_B_refined6.999
r_long_range_B_other6.866
r_scangle_other6.074
r_scbond_it4.369
r_scbond_other4.369
r_mcangle_it3.586
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.594
r_dihedral_angle_4_deg17.982
r_dihedral_angle_3_deg12.858
r_dihedral_angle_1_deg7.384
r_long_range_B_refined6.999
r_long_range_B_other6.866
r_scangle_other6.074
r_scbond_it4.369
r_scbond_other4.369
r_mcangle_it3.586
r_mcangle_other3.586
r_mcbond_it2.908
r_mcbond_other2.903
r_angle_refined_deg1.431
r_angle_other_deg1.267
r_chiral_restr0.069
r_gen_planes_refined0.011
r_bond_refined_d0.007
r_gen_planes_other0.002
r_bond_other_d0.001
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 Atoms6668
Nucleic Acid Atoms
Solvent Atoms786
Heterogen Atoms318

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
REFMACphasing