3AIL | pdb_00003ail

Crystal structure of a HSL-like carboxylesterase from Sulfolobus tokodaii complexed with paraoxon

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	0.1M Tris-HCl pH 8.5, 0.2M Ammonium phosphate monobasic, 50% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.93	58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.323	α = 90
b = 114.367	β = 108.44
c = 101.892	γ = 90

Symmetry
Space Group	P 1 21 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		2009-12-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	1.0	SPring-8	BL38B1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.91	50	96.1	0.049	0.035	23.2	3.1	221504	123521		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.91	1.98	96.9		0.316	0.276	3.6	3	21924

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	3AIK	1.91	28.07	117127	6182	96.1	0.16351	0.16204	0.16	0.19128	0.19	RANDOM	25.094

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	0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.449
r_dihedral_angle_4_deg	16.79
r_dihedral_angle_3_deg	16.461
r_dihedral_angle_1_deg	7.345
r_scangle_it	6.741
r_scbond_it	4.465
r_mcangle_it	2.915
r_mcbond_it	1.951
r_angle_refined_deg	1.118
r_chiral_restr	0.103

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.449
r_dihedral_angle_4_deg	16.79
r_dihedral_angle_3_deg	16.461
r_dihedral_angle_1_deg	7.345
r_scangle_it	6.741
r_scbond_it	4.465
r_mcangle_it	2.915
r_mcbond_it	1.951
r_angle_refined_deg	1.118
r_chiral_restr	0.103
r_gen_planes_refined	0.018
r_bond_refined_d	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8948
Nucleic Acid Atoms
Solvent Atoms	664
Heterogen Atoms	84

Software

Software
Software Name	Purpose
BL38B1	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	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.