9J5D

ESTS1 phthalate ester degrading esterase from Sulfobacillus acidophilus in complex with dimethyl phthalate on surface

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
2.25	45.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.038	α = 90
b = 108.038	β = 90
c = 44.546	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		2022-09-30	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	1.5	27.7	100	0.158	8.6	3.02		58638

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	1.5	1.53	100		1	1.3

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	25.562	47678	2351	99.878	0.154	0.1512	0.2002	18.264

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]
0.702	0.351		0.702		-2.276

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.945
r_dihedral_angle_2_deg	15.741
r_dihedral_angle_3_deg	14.436
r_dihedral_angle_1_deg	6.049
r_rigid_bond_restr	3.41
r_lrange_it	2.664
r_lrange_other	2.651
r_scangle_it	2.595
r_scangle_other	2.594
r_scbond_it	2.281
r_scbond_other	2.28
r_mcangle_other	1.763
r_mcangle_it	1.76
r_mcbond_it	1.448
r_mcbond_other	1.448
r_angle_refined_deg	1.425
r_angle_other_deg	0.49
r_nbd_other	0.233
r_nbd_refined	0.225
r_symmetry_xyhbond_nbd_refined	0.225
r_symmetry_nbd_refined	0.219
r_symmetry_nbd_other	0.191
r_nbtor_refined	0.182
r_xyhbond_nbd_refined	0.142
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.075
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2303
Nucleic Acid Atoms
Solvent Atoms	190
Heterogen Atoms	44

Software

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