2J7D

Beta-glucosidase from Thermotoga maritima in complex with methoxycarbonyl-substituted glucoimidazole

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 = 94.209	α = 90
b = 94.638	β = 90
c = 113.31	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	ADSC CCD	TOROIDAL MIRROR	2005-02-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2		ESRF	ID14-2

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	2.25	20	99.8	0.07	24.93	4.8		49005

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	2.25	2.33	100		0.4	4.59	4.7

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	2.24	72.55	46475	2478	99	0.179	0.176	0.241	RANDOM	29.88

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]
-0.26					0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.194
r_dihedral_angle_4_deg	19.714
r_dihedral_angle_3_deg	15.331
r_dihedral_angle_1_deg	6.352
r_scangle_it	2.56
r_scbond_it	1.763
r_angle_refined_deg	1.378
r_mcangle_it	1.155
r_mcbond_it	0.703
r_nbtor_refined	0.31
r_symmetry_hbond_refined	0.217
r_nbd_refined	0.197
r_symmetry_vdw_refined	0.185
r_xyhbond_nbd_refined	0.143
r_chiral_restr	0.091
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
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	7157
Nucleic Acid Atoms
Solvent Atoms	527
Heterogen Atoms	41

Software

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