3AI0 | pdb_00003ai0

Crystal structure of beta-glucosidase from termite Neotermes koshunensis in complex with para-nitrophenyl-beta-D-glucopyranoside

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3AHZ	PDB ENTRY 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	43.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.089	α = 90
b = 68.755	β = 95.68
c = 75.746	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 210	Vertically Focusing Mirror	2009-04-22	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	1.4	30	99.5	0.041	31.2	4.5	93699	93220		1	18.6

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)
	1.4	1.45	97.4		0.428	3	4	9350

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 3AHZ	1.4	25.4	84715	4491	95.07	0.12341	0.12184	0.13	0.15304	0.16	RANDOM	13.103

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]
-1.04		-0.3	-0.32		1.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.826
r_dihedral_angle_4_deg	12.564
r_dihedral_angle_3_deg	10.29
r_sphericity_free	7.032
r_dihedral_angle_1_deg	5.485
r_scangle_it	4.402
r_sphericity_bonded	3.766
r_scbond_it	3.119
r_mcangle_it	2.179
r_rigid_bond_restr	1.705

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.826
r_dihedral_angle_4_deg	12.564
r_dihedral_angle_3_deg	10.29
r_sphericity_free	7.032
r_dihedral_angle_1_deg	5.485
r_scangle_it	4.402
r_sphericity_bonded	3.766
r_scbond_it	3.119
r_mcangle_it	2.179
r_rigid_bond_restr	1.705
r_mcbond_it	1.507
r_angle_refined_deg	1.431
r_chiral_restr	0.111
r_gen_planes_refined	0.014
r_bond_refined_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3810
Nucleic Acid Atoms
Solvent Atoms	781
Heterogen Atoms	27

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.