3VII | pdb_00003vii

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

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	0.1 M Bis-Tris, 18-21%(w/v) PEG 3350, 0.1-0.25 M MgCl2, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.02	α = 90
b = 68.472	β = 95.32
c = 74.774	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 315r	Vertically Collimating Premirror, Toroidal Focusing Mirror	2009-01-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL13B1	0.80000	NSRRC	BL13B1

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	0.97	30	98.8	0.052	29.6	4.7	274396	271148		1	10

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	0.97	1	99.6		0.598	2.1	4.5	27341

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	3AHZ	0.97	27.2	270983	13672	98.67	0.12779	0.12687	0.13	0.14501	0.14	RANDOM	12.664

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]
-0.59		-0.43	-0.2		0.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.862
r_dihedral_angle_4_deg	13.984
r_dihedral_angle_3_deg	10.797
r_dihedral_angle_1_deg	5.99
r_scangle_it	3.726
r_scbond_it	2.6
r_mcangle_it	1.853
r_angle_refined_deg	1.406
r_mcbond_it	1.273
r_rigid_bond_restr	1.197
r_chiral_restr	0.096
r_gen_planes_refined	0.01
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	3811
Nucleic Acid Atoms
Solvent Atoms	724
Heterogen Atoms	21

Software

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