9J5C

ESTS1 phthalate ester degrading esterase from Sulfobacillus acidophilus in complex with diethylhexyl 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
2.278	46.049

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.258	α = 90
b = 108.258	β = 90
c = 44.872	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		2023-01-14	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	2.7	25.64	99.9	0.43	15.5	3.06		8440

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	2.7	2.83			1	3.7

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	2.7	23.45	8433	424	99.834	0.218	0.214	0.2945	5

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]
0.405	0.202		0.405		-1.313

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.429
r_dihedral_angle_6_deg	13.912
r_dihedral_angle_2_deg	9.299
r_dihedral_angle_1_deg	7.306
r_angle_refined_deg	1.148
r_angle_other_deg	0.369
r_nbd_refined	0.216
r_symmetry_xyhbond_nbd_refined	0.215
r_symmetry_nbd_other	0.201
r_nbd_other	0.184
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.179
r_symmetry_nbd_refined	0.142
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.052
r_symmetry_xyhbond_nbd_other	0.028
r_rigid_bond_restr	0.012
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_lrange_it
r_lrange_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2287
Nucleic Acid Atoms
Solvent Atoms	84
Heterogen Atoms	56

Software

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