7P32

Crystal structure of human lysosomal acid-alpha-glucosidase, GAA, in complex with cyclosulfamidate 6


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 PH 7.0, 2% V/V PEG400
Crystal Properties
Matthews coefficientSolvent content
3.464

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.043α = 90
b = 102.606β = 90
c = 129.118γ = 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 20.98009SOLEILPROXIMA 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
11.8247.6899.80.10.1080.040.99915.913.511588923.36
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.821.8596.20.7050.4921.511.7

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-VALUE5NN41.8247115802579199.7910.1510.15130.150.1754taken over from 5NN429.022
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]
0.589-0.326-0.263
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.285
r_dihedral_angle_4_deg17.525
r_dihedral_angle_3_deg12.189
r_lrange_it7.295
r_lrange_other7.264
r_scangle_it6.787
r_scangle_other6.787
r_dihedral_angle_1_deg6.771
r_scbond_it4.923
r_scbond_other4.923
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.285
r_dihedral_angle_4_deg17.525
r_dihedral_angle_3_deg12.189
r_lrange_it7.295
r_lrange_other7.264
r_scangle_it6.787
r_scangle_other6.787
r_dihedral_angle_1_deg6.771
r_scbond_it4.923
r_scbond_other4.923
r_mcangle_it3.503
r_mcangle_other3.503
r_mcbond_it2.998
r_mcbond_other2.989
r_angle_refined_deg1.509
r_angle_other_deg1.366
r_symmetry_xyhbond_nbd_refined0.23
r_nbd_other0.225
r_nbd_refined0.196
r_symmetry_nbd_other0.185
r_nbtor_refined0.17
r_xyhbond_nbd_refined0.17
r_symmetry_nbd_refined0.15
r_symmetry_nbtor_other0.085
r_chiral_restr0.078
r_symmetry_xyhbond_nbd_other0.03
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6668
Nucleic Acid Atoms
Solvent Atoms680
Heterogen Atoms237

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing