3GXP

Crystal structure of acid-alpha-galactosidase A complexed with galactose at pH 4.5

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION			vapor diffusion

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.51	α = 90
b = 89.51	β = 90
c = 215.927	γ = 120

Symmetry
Space Group	P 32 2 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	2.2	76.6					42395

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	2.2	38.15	42395	2144	81.9	0.204	0.201	0.265	RANDOM	71.47

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]
1.29	0.64		1.29		-1.93

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.571
r_dihedral_angle_3_deg	19.863
r_dihedral_angle_4_deg	19.14
r_dihedral_angle_1_deg	8.082
r_scangle_it	3.374
r_scbond_it	2.392
r_angle_refined_deg	2.049
r_mcangle_it	1.392
r_mcbond_it	0.929
r_nbtor_refined	0.315

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.571
r_dihedral_angle_3_deg	19.863
r_dihedral_angle_4_deg	19.14
r_dihedral_angle_1_deg	8.082
r_scangle_it	3.374
r_scbond_it	2.392
r_angle_refined_deg	2.049
r_mcangle_it	1.392
r_mcbond_it	0.929
r_nbtor_refined	0.315
r_symmetry_vdw_refined	0.28
r_nbd_refined	0.226
r_symmetry_hbond_refined	0.195
r_xyhbond_nbd_refined	0.15
r_chiral_restr	0.148
r_bond_refined_d	0.02
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6253
Nucleic Acid Atoms
Solvent Atoms	157
Heterogen Atoms	256

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.