3GXF

Crystal structure of acid-beta-glucosidase with isofagomine at neutral pH

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	298	0.8 M NaH2PO4, 0.8 M KH2PO4, 0.1 M Hepes pH 7.5, SOAK with 500uM isofagomine for 10 min, glycerol in cryo, VAPOR DIFFUSION, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.24	62.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.311	α = 90
b = 92.013	β = 111.21
c = 152.362	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray						M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D		APS	23-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.4	32.12					103572

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	PDB entry '2NSX	2.4	32.12	98363	103572	5209	93.17	0.182	0.178	0.245	RANDOM	27.274

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]
0.2		-0.17	-0.18		-0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.898
r_dihedral_angle_4_deg	20.705
r_dihedral_angle_3_deg	17.889
r_dihedral_angle_1_deg	8.265
r_scangle_it	3.684
r_scbond_it	2.398
r_angle_refined_deg	1.957
r_mcangle_it	1.659
r_mcbond_it	0.978
r_xyhbond_nbd_refined	0.335
r_nbtor_refined	0.313
r_nbd_refined	0.229
r_symmetry_vdw_refined	0.198
r_symmetry_hbond_refined	0.184
r_chiral_restr	0.134
r_bond_refined_d	0.02
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15720
Nucleic Acid Atoms
Solvent Atoms	905
Heterogen Atoms	426

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction