7P32

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5NN4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	1.9 M AMMONIUM SULPHATE, 0.1 M HEPES PH 7.0, 2% V/V PEG400

Crystal Properties
Matthews coefficient	Solvent content
3.4	64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.043	α = 90
b = 102.606	β = 90
c = 129.118	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 9M		2019-09-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 2	0.98009	SOLEIL	PROXIMA 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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.82	47.68	99.8	0.1	0.108	0.04	0.999	15.9	13.5		115889			23.36

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.82	1.85	96.2		0.705	0.492	1.5	11.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	FREE R-VALUE	5NN4	1.82	47	115802	5791	99.791	0.151	0.1513	0.15	0.1754	taken over from 5NN4	29.022

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
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.285
r_dihedral_angle_4_deg	17.525
r_dihedral_angle_3_deg	12.189
r_lrange_it	7.295
r_lrange_other	7.264
r_scangle_it	6.787
r_scangle_other	6.787
r_dihedral_angle_1_deg	6.771
r_scbond_it	4.923
r_scbond_other	4.923
r_mcangle_it	3.503
r_mcangle_other	3.503
r_mcbond_it	2.998
r_mcbond_other	2.989
r_angle_refined_deg	1.509
r_angle_other_deg	1.366
r_symmetry_xyhbond_nbd_refined	0.23
r_nbd_other	0.225
r_nbd_refined	0.196
r_symmetry_nbd_other	0.185
r_nbtor_refined	0.17
r_xyhbond_nbd_refined	0.17
r_symmetry_nbd_refined	0.15
r_symmetry_nbtor_other	0.085
r_chiral_restr	0.078
r_symmetry_xyhbond_nbd_other	0.03
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6668
Nucleic Acid Atoms
Solvent Atoms	680
Heterogen Atoms	237

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
REFMAC	phasing