4ZOB

Crystal Structure of beta-glucosidase from Listeria innocua in complex with gluconolactone

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	PEG 4000, NaCl, LiSO4, glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.88	57.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.36	α = 90
b = 95.81	β = 97.2
c = 213.31	γ = 90

Symmetry
Space Group	I 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		2013-06-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.0	Photon Factory	AR-NW12A

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	2.4	41.91	100	6.8	3.6		67092

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	4ZOE	2.4	41.91	67092	3569	99.92	0.174	0.1699	0.2501	RANDOM	32.537

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]
0.01		0.02	-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.367
r_sphericity_free	20.349
r_dihedral_angle_4_deg	20.19
r_dihedral_angle_3_deg	16.194
r_sphericity_bonded	8.114
r_dihedral_angle_1_deg	6.608
r_rigid_bond_restr	4.179
r_angle_other_deg	2.091
r_angle_refined_deg	1.636
r_chiral_restr	0.081

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.367
r_sphericity_free	20.349
r_dihedral_angle_4_deg	20.19
r_dihedral_angle_3_deg	16.194
r_sphericity_bonded	8.114
r_dihedral_angle_1_deg	6.608
r_rigid_bond_restr	4.179
r_angle_other_deg	2.091
r_angle_refined_deg	1.636
r_chiral_restr	0.081
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_gen_planes_other	0.004
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11148
Nucleic Acid Atoms
Solvent Atoms	367
Heterogen Atoms	116

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.