3GXM | pdb_00003gxm

Crystal structure of acid-beta-glucosidase at pH 4.5, phosphate crystallization condition

X-RAY DIFFRACTION

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
3.24	62.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.505	α = 90
b = 91.779	β = 111.24
c = 152.751	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 14-BM-C		APS	14-BM-C

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	34.34					138784

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		THROUGHOUT	2.2	34.34	138784	6970	96.33	0.223	0.22	0.2199	0.276	0.2737	RANDOM	25.106

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]
-0.01					0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.157
r_dihedral_angle_4_deg	21.807
r_dihedral_angle_3_deg	17.716
r_dihedral_angle_1_deg	7.689
r_scangle_it	3.084
r_scbond_it	2.053
r_angle_refined_deg	1.682
r_mcangle_it	1.394
r_mcbond_it	0.823
r_xyhbond_nbd_refined	0.312

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.157
r_dihedral_angle_4_deg	21.807
r_dihedral_angle_3_deg	17.716
r_dihedral_angle_1_deg	7.689
r_scangle_it	3.084
r_scbond_it	2.053
r_angle_refined_deg	1.682
r_mcangle_it	1.394
r_mcbond_it	0.823
r_xyhbond_nbd_refined	0.312
r_nbtor_refined	0.309
r_symmetry_hbond_refined	0.217
r_nbd_refined	0.216
r_symmetry_vdw_refined	0.192
r_chiral_restr	0.115
r_bond_refined_d	0.016
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15720
Nucleic Acid Atoms
Solvent Atoms	1144
Heterogen Atoms	196

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 R01GM157729.