9J5A

ESTS1 phthalate ester degrading esterase from Sulfobacillus acidophilus in complex with p-nitrophenol

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	45.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.156	α = 90
b = 108.156	β = 90
c = 44.549	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		2022-09-29	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	25.98	100	0.13	14.7	3.19		47847

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	99.4		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	23.427	47831	2365	99.939	0.128	0.1257	0.1766	14.289

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]
-0.098	-0.049		-0.098		0.319

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.031
r_dihedral_angle_3_deg	14.554
r_mcangle_it	7.451
r_mcangle_other	7.448
r_mcbond_it	7.32
r_mcbond_other	7.317
r_scangle_it	7.055
r_scangle_other	7.054
r_dihedral_angle_2_deg	6.764
r_lrange_it	6.394
r_lrange_other	6.261
r_dihedral_angle_1_deg	6.239
r_scbond_it	5.171
r_scbond_other	5.17
r_rigid_bond_restr	3.725
r_angle_refined_deg	1.392
r_angle_other_deg	0.498
r_nbd_refined	0.226
r_symmetry_xyhbond_nbd_refined	0.22
r_symmetry_nbd_other	0.187
r_symmetry_nbd_refined	0.187
r_nbtor_refined	0.18
r_nbd_other	0.172
r_xyhbond_nbd_refined	0.152
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.076
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.005
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2312
Nucleic Acid Atoms
Solvent Atoms	206
Heterogen Atoms	103

Software

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