4ZO8 | pdb_00004zo8

Crystal Structure of mutant (D270A) beta-glucosidase from Listeria innocua in complex with sophorose

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4ZOE

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
2.85	56.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.58	α = 90
b = 94.73	β = 96.29
c = 215.112	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		2014-05-26	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	32.5	97.6	5.4	3.3		117573

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	4ZOE	2	32.5	111659	5914	97.46	0.2056	0.2024	0.21	0.2674	0.27	RANDOM	17.756

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

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.192
r_dihedral_angle_4_deg	20.145
r_sphericity_free	18.016
r_dihedral_angle_3_deg	14.611
r_dihedral_angle_1_deg	6.68
r_sphericity_bonded	5.976
r_rigid_bond_restr	5.493
r_angle_other_deg	2.201
r_angle_refined_deg	1.72
r_chiral_restr	0.098

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.192
r_dihedral_angle_4_deg	20.145
r_sphericity_free	18.016
r_dihedral_angle_3_deg	14.611
r_dihedral_angle_1_deg	6.68
r_sphericity_bonded	5.976
r_rigid_bond_restr	5.493
r_angle_other_deg	2.201
r_angle_refined_deg	1.72
r_chiral_restr	0.098
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_gen_planes_other	0.008
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11184
Nucleic Acid Atoms
Solvent Atoms	602
Heterogen Atoms	48

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.