8ZE9 | pdb_00008ze9

ESTS1 phthalate ester degrading esterase from Sulfobacillus acidophilus S154A mutant in complex with diethylhexyl phthalate at 2.4A

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8.5	293.15	Lithium sulphate, 0.1M Tris, Ammonium sulphate

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.342

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.499	α = 90
b = 107.499	β = 90
c = 44.919	γ = 120

Symmetry
Space Group	P 63

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	RIGAKU HyPix-6000HE		2024-03-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	23.073	100	0.145	0.997	12.8	15.2		11809

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.49			0.337	0.957

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.4	23.073	11791	589	99.772	0.176	0.1728	0.1736	0.2464	0.2475	23.408

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]
0.717	0.359		0.717		-2.327

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.312
r_dihedral_angle_6_deg	13.815
r_lrange_it	7.337
r_dihedral_angle_2_deg	6.976
r_dihedral_angle_1_deg	6.362
r_scangle_it	3.908
r_scbond_it	2.53
r_mcangle_it	2.484
r_mcbond_it	1.538
r_angle_refined_deg	1.456

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.312
r_dihedral_angle_6_deg	13.815
r_lrange_it	7.337
r_dihedral_angle_2_deg	6.976
r_dihedral_angle_1_deg	6.362
r_scangle_it	3.908
r_scbond_it	2.53
r_mcangle_it	2.484
r_mcbond_it	1.538
r_angle_refined_deg	1.456
r_nbtor_refined	0.312
r_symmetry_nbd_refined	0.247
r_nbd_refined	0.228
r_xyhbond_nbd_refined	0.175
r_symmetry_xyhbond_nbd_refined	0.111
r_chiral_restr	0.108
r_bond_refined_d	0.006
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2294
Nucleic Acid Atoms
Solvent Atoms	73
Heterogen Atoms	60

Software

Software
Software Name	Purpose
REFMAC	refinement
CrysalisPro	data reduction
Aimless	data scaling
MOLREP	phasing

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.