7P2Z | pdb_00007p2z

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

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 REMARK 280 PH 7.0, 2% V/V PEG400

Crystal Properties
Matthews coefficient	Solvent content
3.4	63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.157	α = 90
b = 102.539	β = 90
c = 129.048	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	0.9801	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	1.85	47.65	100	0.121	0.13	0.049	0.998	14.5	13.6		110461			20.85

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)	Redundancy	Number Unique Reflections (All)
1	1.85	1.88	99.9		1.554	0.628	0.742	2.1

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	FREE R-VALUE	5nn4	1.85	47	110373	5503	99.952	0.15	0.14978	0.1485	0.16	0.1753	0.19	taken over form entry 5NN4	28.703

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
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.274
r_dihedral_angle_4_deg	15.751
r_scbond_it	12.111
r_scbond_other	12.11
r_dihedral_angle_3_deg	11.954
r_scangle_it	11.857
r_scangle_other	11.856
r_lrange_other	10.882
r_lrange_it	10.829
r_dihedral_angle_1_deg	6.846
r_mcangle_it	4.97
r_mcangle_other	4.969
r_mcbond_it	4.642
r_mcbond_other	4.641
r_angle_refined_deg	1.513
r_angle_other_deg	1.355
r_nbd_other	0.242
r_nbd_refined	0.194
r_symmetry_nbd_other	0.184
r_xyhbond_nbd_refined	0.179
r_nbtor_refined	0.17
r_symmetry_xyhbond_nbd_refined	0.161
r_symmetry_nbd_refined	0.147
r_symmetry_xyhbond_nbd_other	0.092
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.077
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6691
Nucleic Acid Atoms
Solvent Atoms	778
Heterogen Atoms	265

Software

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