2J77

Beta-glucosidase from Thermotoga maritima in complex with deoxynojirimycin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1OD0	PDB ENTRY 1OD0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7		10 MG/ML PROTEIN. 15% PEG 4K, 0.1 M IMIDAZOLE, PH 7, 0.2 M CALCIUM ACETATE. 25% ETHYLENE GLYCOL AS CRYO.

Crystal Properties
Matthews coefficient	Solvent content
2.3	47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.563	α = 90
b = 94.365	β = 90
c = 112.952	γ = 90

Symmetry
Space Group	P 21 21 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	TOROIDAL MIRROR	2004-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-3		ESRF	ID14-3

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	2.1	30	100	0.07	23.42	5.6		58779

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	2.1	2.18	100		0.37	4.7	5.6

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1OD0	2.1	72.55	55710	2970	99.7	0.199	0.196	0.258	RANDOM	32.69

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]
0.21			0.61		-0.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.035
r_dihedral_angle_4_deg	18.333
r_dihedral_angle_3_deg	14.697
r_dihedral_angle_1_deg	6.195
r_scangle_it	2.495
r_scbond_it	1.706
r_angle_refined_deg	1.294
r_mcangle_it	1.157
r_mcbond_it	0.699
r_nbtor_refined	0.313
r_symmetry_hbond_refined	0.212
r_nbd_refined	0.203
r_symmetry_vdw_refined	0.181
r_xyhbond_nbd_refined	0.14
r_chiral_restr	0.089
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7143
Nucleic Acid Atoms
Solvent Atoms	505
Heterogen Atoms	27

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling