9GSV | pdb_00009gsv

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


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 = 96.372α = 90
b = 102.298β = 90
c = 128.155γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2018-05-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 10.978570SOLEILPROXIMA 1

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
11.848.2399.90.0910.0990.0390.99811.36.611761826.2
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)
11.81.831.3781.4920.5690.5361.36.7

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-VALUE1.848.23111674585599.840.161920.160380.17110.191680.2025Taken over from parent data set30.96
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]
0.98-0.22-0.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.114
r_dihedral_angle_4_deg16.356
r_dihedral_angle_3_deg12.104
r_long_range_B_other9.432
r_long_range_B_refined9.412
r_scangle_other9.337
r_scbond_it7.434
r_scbond_other7.433
r_dihedral_angle_1_deg7.127
r_mcangle_it4.502
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.114
r_dihedral_angle_4_deg16.356
r_dihedral_angle_3_deg12.104
r_long_range_B_other9.432
r_long_range_B_refined9.412
r_scangle_other9.337
r_scbond_it7.434
r_scbond_other7.433
r_dihedral_angle_1_deg7.127
r_mcangle_it4.502
r_mcangle_other4.502
r_mcbond_it4.016
r_mcbond_other4.009
r_angle_refined_deg1.592
r_angle_other_deg1.392
r_chiral_restr0.082
r_gen_planes_refined0.013
r_bond_refined_d0.011
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 Atoms6631
Nucleic Acid Atoms
Solvent Atoms475
Heterogen Atoms293

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
REFMACphasing