9J1V

ESTS1 phthalate ester degrading esterase from Sulfobacillus acidophilus in complex with Monomethyl 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), Jeffamine ED-2001

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.984	α = 90
b = 107.984	β = 90
c = 44.782	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		2022-08-18	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	2	27.74	100	0.143	18.8	2.8		20399

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	2	2.05			0.517	7.8

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	25.95	20382	963	99.892	0.113	0.1082	0.201	19.039

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]
0.589	0.295		0.589		-1.912

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.137
r_dihedral_angle_2_deg	15.774
r_dihedral_angle_3_deg	15.125
r_rigid_bond_restr	9.008
r_scangle_it	7.835
r_scangle_other	7.834
r_lrange_it	7.083
r_lrange_other	7.061
r_scbond_it	6.822
r_scbond_other	6.811
r_dihedral_angle_1_deg	6.516
r_mcangle_it	4.774
r_mcangle_other	4.773
r_mcbond_it	3.99
r_mcbond_other	3.969
r_angle_refined_deg	1.672
r_angle_other_deg	0.576
r_nbd_refined	0.227
r_symmetry_nbd_other	0.194
r_symmetry_nbd_refined	0.184
r_nbtor_refined	0.181
r_nbd_other	0.18
r_xyhbond_nbd_refined	0.154
r_symmetry_xyhbond_nbd_refined	0.118
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.081
r_bond_refined_d	0.014
r_gen_planes_refined	0.009
r_bond_other_d	0.004
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2279
Nucleic Acid Atoms
Solvent Atoms	115
Heterogen Atoms	67

Software

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