3AHZ | pdb_00003ahz

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

X-RAY DIFFRACTION

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Starting Model(s)

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

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
2.14	42.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.959	α = 90
b = 68.451	β = 95.53
c = 75.228	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	IMAGE PLATE	MAR scanner 345 mm plate	Vertically Focusing Mirror	2008-08-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL13C1	0.97315	NSRRC	BL13C1

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	1.34	30	99.9	0.054	29.7	5.7	105275	105222		1	16.2

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)
	1.34	1.39	99.7		0.469	3.9	5.5	10460

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	PDB ENTRY 1CBG	1.34	25.6	95986	5061	96.07	0.11671	0.11526	0.1203	0.14381	0.1494	RANDOM	11.842

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]
-0.65		-0.58	-0.2		0.75

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.012
r_dihedral_angle_4_deg	13.711
r_dihedral_angle_3_deg	10.651
r_sphericity_free	7.024
r_dihedral_angle_1_deg	5.88
r_scangle_it	4.221
r_sphericity_bonded	3.569
r_scbond_it	2.996
r_mcangle_it	2.113
r_rigid_bond_restr	1.607
r_angle_refined_deg	1.525
r_mcbond_it	1.469
r_chiral_restr	0.101
r_gen_planes_refined	0.01
r_bond_refined_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3811
Nucleic Acid Atoms
Solvent Atoms	806
Heterogen Atoms	14

Software

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