4I3G

Crystal Structure of DesR, a beta-glucosidase from Streptomyces venezuelae in complex with D-glucose.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3AC0	PDB entry 3AC0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	1.3 M ammonium sulfate, 300 mM potassium chloride, 25 mM glucose, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.51	50.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 131.269	α = 90
b = 198.314	β = 90
c = 67.023	γ = 90

Symmetry
Space Group	P 21 21 2

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		2012-08-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.979	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	94.1		6.4	324839	324839

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.45	96.7		0.38	2.8	4.2	32626

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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 3AC0	1.4	30	324820	308445	16375	94.65	0.17336	0.17202	0.19876	RANDOM	21.206

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]
0.17			-0.5		0.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.578
r_dihedral_angle_4_deg	18.062
r_dihedral_angle_3_deg	11.532
r_dihedral_angle_1_deg	6.591
r_scangle_it	5.33
r_scbond_it	3.431
r_mcangle_it	2.314
r_angle_refined_deg	1.952
r_mcbond_it	1.506
r_chiral_restr	0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.578
r_dihedral_angle_4_deg	18.062
r_dihedral_angle_3_deg	11.532
r_dihedral_angle_1_deg	6.591
r_scangle_it	5.33
r_scbond_it	3.431
r_mcangle_it	2.314
r_angle_refined_deg	1.952
r_mcbond_it	1.506
r_chiral_restr	0.13
r_bond_refined_d	0.012
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11537
Nucleic Acid Atoms
Solvent Atoms	1541
Heterogen Atoms	126

Software

Software
Software Name	Purpose
HKL-3000	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

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.