9GTL | pdb_00009gtl

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5NN3

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
3.4	63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.315	α = 90
b = 102.67	β = 90
c = 126.808	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 16M		2020-07-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.978565	SOLEIL	PROXIMA 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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2	47.58	100	0.143	0.149	0.04	0.999	12.2	13.7		83802

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)	Redundancy	Number Unique Reflections (All)
1	2	2.04		100	2.436	2.527	0.669	0.505		14.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (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 Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	2	47.2	79540	4183	99.95	0.16914	0.16752	0.1752	0.19975	0.2054	Taken over from parent data set	40.695

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]
2.74			-2.17		-0.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.117
r_dihedral_angle_4_deg	14.595
r_dihedral_angle_3_deg	12.466
r_dihedral_angle_1_deg	7.108
r_long_range_B_refined	7.085
r_long_range_B_other	7.065
r_scangle_other	6.213
r_scbond_it	4.243
r_scbond_other	4.242
r_mcangle_it	4.002
r_mcangle_other	4.002
r_mcbond_it	3.027
r_mcbond_other	3.024
r_angle_refined_deg	1.319
r_angle_other_deg	1.251
r_chiral_restr	0.065
r_gen_planes_refined	0.009
r_bond_refined_d	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001
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 Atoms	Number
Protein Atoms	6631
Nucleic Acid Atoms
Solvent Atoms	485
Heterogen Atoms	238

Software

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