4ZOE | pdb_00004zoe

Crystal Structure of beta-glucosidase from Listeria innocua

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1EX1

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
2.86	57.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.75	α = 90
b = 95.1	β = 96.34
c = 214.996	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		2012-11-20	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	1.8	28.38	98.5	8.2	4.9		163230

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	1EX1	1.8	28.17	154994	8215	98.28	0.183	0.1801	0.1904	0.2398	0.2473	RANDOM	14.86

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]
0.02		0.02	-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.051
r_dihedral_angle_4_deg	18.857
r_sphericity_free	18.123
r_dihedral_angle_3_deg	13.732
r_dihedral_angle_1_deg	6.749
r_sphericity_bonded	5.574
r_rigid_bond_restr	4.595
r_angle_other_deg	2.042
r_angle_refined_deg	2.021
r_chiral_restr	0.126
r_bond_refined_d	0.021
r_gen_planes_other	0.011
r_gen_planes_refined	0.01
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11190
Nucleic Acid Atoms
Solvent Atoms	1173
Heterogen Atoms	26

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction