2NT0 | pdb_00002nt0

Acid-beta-glucosidase low pH, glycerol bound

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1OGS	1OGS monomer

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	298	1 M Ammonium Sulfate 0.17 M Guanidinium HCl 0.02 M KCl 0.1 M Acetate buffer pH 4.5 Cryoprotectant includes 20% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.17	61.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.941	α = 90
b = 91.759	β = 110.96
c = 152.81	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		2005-09-30	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	1.8	50	84.8	0.062	7.6	2.1		220956			24.35

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.86	71.8		0.417	1.5	1.8	18569

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	1OGS monomer	1.79	50	220955	11117	84.13	0.181	0.179	0.1803	0.215	0.2172	RANDOM	24.352

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]
2.15		-0.33	-1.24		-1.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.931
r_dihedral_angle_4_deg	18.413
r_dihedral_angle_3_deg	14.367
r_dihedral_angle_1_deg	6.833
r_scangle_it	3.622
r_scbond_it	2.485
r_angle_refined_deg	1.585
r_mcangle_it	1.53
r_mcbond_it	1.011
r_nbtor_refined	0.308
r_nbd_refined	0.219
r_symmetry_vdw_refined	0.2
r_xyhbond_nbd_refined	0.197
r_symmetry_hbond_refined	0.165
r_chiral_restr	0.115
r_bond_refined_d	0.017
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15720
Nucleic Acid Atoms
Solvent Atoms	1710
Heterogen Atoms	248

Software

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