9J5B

ESTS1 phthalate ester degrading esterase from Sulfobacillus acidophilus in complex with Dimethyl 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	7	293.15	Sodium malonate, 0.1 M HEPES (pH 7.0), Jeffamine ED-2001

Crystal Properties
Matthews coefficient	Solvent content
2.234	44.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.668	α = 90
b = 107.668	β = 90
c = 44.489	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		2022-10-12	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)	Rrim I (All)	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	1.6	25.48	100	0.18	12.4	3.28		47379

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.63	100		1	1.2

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	1.6	25.48	39076	1848	99.959	0.15	0.1475	0.194	8.656

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]
-0.047	-0.024		-0.047		0.153

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	17.785
r_dihedral_angle_6_deg	16.231
r_dihedral_angle_3_deg	14.646
r_dihedral_angle_1_deg	6.167
r_rigid_bond_restr	3.637
r_lrange_other	2.831
r_lrange_it	2.822
r_scangle_it	2.725
r_scangle_other	2.724
r_scbond_it	2.358
r_scbond_other	2.357
r_mcangle_other	1.711
r_mcangle_it	1.701
r_angle_refined_deg	1.442
r_mcbond_it	1.335
r_mcbond_other	1.335
r_angle_other_deg	0.489
r_symmetry_nbd_refined	0.237
r_nbd_other	0.228
r_nbd_refined	0.222
r_symmetry_xyhbond_nbd_refined	0.214
r_symmetry_nbd_other	0.189
r_nbtor_refined	0.181
r_xyhbond_nbd_refined	0.171
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.074
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2313
Nucleic Acid Atoms
Solvent Atoms	162
Heterogen Atoms	91

Software

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