2NT1 | pdb_00002nt1

Structure of acid-beta-glucosidase at neutral pH

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2NT0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	0.8 M Na dihydrogen phosphate 0.8 M K dihydrogen phosphate 0.1 M Hepes buffer pH 7.5 Cryoprotected in 2 M Lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.25	62.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.185	α = 90
b = 91.792	β = 110.91
c = 153.036	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	100	CCD	MARRESEARCH		2006-06-30	M	SINGLE WAVELENGTH

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

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (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	2.3	20	95.1	0.106	7.8	3.5		119558			29.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.38	79.6		0.454	2.4	2.9	9993

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2NT0	2.3	19.94	119536	6021	94.83	0.178	0.175	0.18	0.24	0.24	RANDOM	29.096

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]
-0.07		0.06	-0.09		0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.509
r_dihedral_angle_4_deg	23.386
r_dihedral_angle_3_deg	17.744
r_dihedral_angle_1_deg	8.18
r_scangle_it	4.083
r_scbond_it	2.766
r_angle_refined_deg	1.969
r_mcangle_it	1.798
r_mcbond_it	1.095
r_nbtor_refined	0.311

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.509
r_dihedral_angle_4_deg	23.386
r_dihedral_angle_3_deg	17.744
r_dihedral_angle_1_deg	8.18
r_scangle_it	4.083
r_scbond_it	2.766
r_angle_refined_deg	1.969
r_mcangle_it	1.798
r_mcbond_it	1.095
r_nbtor_refined	0.311
r_xyhbond_nbd_refined	0.236
r_nbd_refined	0.223
r_symmetry_vdw_refined	0.171
r_symmetry_hbond_refined	0.158
r_chiral_restr	0.135
r_bond_refined_d	0.022
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15720
Nucleic Acid Atoms
Solvent Atoms	1344
Heterogen Atoms	446

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
HKL-2000	data reduction

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.