Experiment: 2X41

Structure of beta-glucosidase 3B from Thermotoga neapolitana in complex with glucose

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2X40	PDB ENTRY 2X40

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.4	293	3-5 MG/ML PROTEIN, 16-18 % PEG 3350, 0.2 M NABR, 90 MM BIS-TRIS PROPANE PH 7.4, 20C

Crystal Properties
Matthews coefficient	Solvent content
2.57	57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.13	α = 90
b = 128.46	β = 90
c = 176.29	γ = 90

Symmetry
Space Group	C 2 2 21

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	MULTILAYER MIRRORS	2008-09-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I911-3		MAX II	I911-3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.05	26.7	98.6	0.06	14.1	3.4		53087			33.4

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	2.05	2.1	99.6		0.67	2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 2X40	2.05	26.719	1.99	53081	2693	98.63	0.1889	0.187	0.1812	0.2251	0.2192	47.3

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]
-1.3823			4.7735		-3.3911

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	16.81
f_angle_d	0.776
f_chiral_restr	0.055
f_bond_d	0.004
f_plane_restr	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5679
Nucleic Acid Atoms
Solvent Atoms	353
Heterogen Atoms	16

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing
PHENIX	phasing
PHENIX	refinement