7P2Z

Crystal structure of human lysosomal acid-alpha-glucosidase, GAA, in complex with cyclosulfamidate 4


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5NN4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72931.9 M AMMONIUM SULPHATE, 0.1 M HEPES REMARK 280 PH 7.0, 2% V/V PEG400
Crystal Properties
Matthews coefficientSolvent content
3.463

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.157α = 90
b = 102.539β = 90
c = 129.048γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2019-09-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 20.9801SOLEILPROXIMA 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
11.8547.651000.1210.130.0490.99814.513.611046120.85
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)RedundancyNumber Unique Reflections (All)
11.851.8899.91.5540.6280.7422.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISFREE R-VALUE5nn41.8547110373550399.9520.150.149780.14850.1753taken over form entry 5NN428.703
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]
1.237-0.8-0.437
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.274
r_dihedral_angle_4_deg15.751
r_scbond_it12.111
r_scbond_other12.11
r_dihedral_angle_3_deg11.954
r_scangle_it11.857
r_scangle_other11.856
r_lrange_other10.882
r_lrange_it10.829
r_dihedral_angle_1_deg6.846
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.274
r_dihedral_angle_4_deg15.751
r_scbond_it12.111
r_scbond_other12.11
r_dihedral_angle_3_deg11.954
r_scangle_it11.857
r_scangle_other11.856
r_lrange_other10.882
r_lrange_it10.829
r_dihedral_angle_1_deg6.846
r_mcangle_it4.97
r_mcangle_other4.969
r_mcbond_it4.642
r_mcbond_other4.641
r_angle_refined_deg1.513
r_angle_other_deg1.355
r_nbd_other0.242
r_nbd_refined0.194
r_symmetry_nbd_other0.184
r_xyhbond_nbd_refined0.179
r_nbtor_refined0.17
r_symmetry_xyhbond_nbd_refined0.161
r_symmetry_nbd_refined0.147
r_symmetry_xyhbond_nbd_other0.092
r_symmetry_nbtor_other0.082
r_chiral_restr0.077
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6691
Nucleic Acid Atoms
Solvent Atoms778
Heterogen Atoms265

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing