3VIK

Crystal structure of beta-glucosidase from termite Neotermes koshunensis in complex with cellobiose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3AHZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	298	0.1M Bis-Tris, 18-21%(w/v) PEG 3350, 0.1-0.25M MgCl2, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.965	α = 90
b = 68.714	β = 95.73
c = 75.832	γ = 90

Symmetry
Space Group	C 1 2 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	ADSC QUANTUM 210r	Vertically Collimating Premirror, Toroidal Focusing Mirror	2010-07-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL12B2	0.90000	SPring-8	BL12B2

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	1.1	30	99.9	0.064	23.4	4.9	190851	190640		1	13.8

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	1.1	1.14	100		0.508	2.4	4.8	19015

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	3AHZ	1.1	22.95	190485	9575	99.54	0.14829	0.14723	0.16824	RANDOM	15.063

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]
-0.95		-0.56	-0.6		1.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.178
r_dihedral_angle_4_deg	15.371
r_dihedral_angle_3_deg	11.241
r_dihedral_angle_1_deg	5.834
r_scangle_it	3.748
r_scbond_it	2.651
r_mcangle_it	1.858
r_angle_refined_deg	1.424
r_mcbond_it	1.314
r_rigid_bond_restr	1.29
r_chiral_restr	0.1
r_gen_planes_refined	0.009
r_bond_refined_d	0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3808
Nucleic Acid Atoms
Solvent Atoms	624
Heterogen Atoms	29

Software

Software
Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling