9J1G

ESTS1 phthalate ester degrading esterase from Sulfobacillus acidophilus in complex with phthalate

X-RAY DIFFRACTION

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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		293.15	Sodium malonate, 0.1 M HEPES (pH 7.0), and Jeffamine ED-2001

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.386	α = 90
b = 108.386	β = 90
c = 44.628	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		2022-08-20	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)	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	1.5	27.12	99.2	0.2	15.7	2.87		48160

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.53	99.7		1.375	2.2

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.5	27.111	48144	2385	99.961	0.12	0.1179	0.1627	14.354

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]
-0.531	-0.265		-0.531		1.721

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.516
r_dihedral_angle_3_deg	13.988
r_dihedral_angle_2_deg	7.961
r_rigid_bond_restr	7.197
r_lrange_it	6.121
r_dihedral_angle_1_deg	6.08
r_lrange_other	5.382
r_scangle_it	5.25
r_scangle_other	5.249
r_scbond_other	4.811
r_scbond_it	4.808
r_mcangle_other	2.912
r_mcangle_it	2.886
r_mcbond_it	2.228
r_mcbond_other	2.228
r_angle_refined_deg	1.557
r_angle_other_deg	0.525
r_symmetry_nbd_refined	0.246
r_nbd_refined	0.228
r_symmetry_xyhbond_nbd_refined	0.211
r_symmetry_nbd_other	0.184
r_nbtor_refined	0.181
r_xyhbond_nbd_refined	0.181
r_nbd_other	0.174
r_chiral_restr	0.083
r_symmetry_nbtor_other	0.077
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_symmetry_xyhbond_nbd_other	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2295
Nucleic Acid Atoms
Solvent Atoms	315
Heterogen Atoms	60

Software

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