9J57

ESTS1 phthalate ester degrading esterase from Sulfobacillus acidophilus in complex with paranitrophenyl butyrate

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
2.259	45.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.048	α = 90
b = 108.048	β = 90
c = 44.672	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		2023-01-13	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	1.8	27.73	100	0.04	15.2	3.93		27832

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	1.8	1.84	100		1	2.4

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	1.8	23.404	27816	1276	99.928	0.125	0.1217	0.1854	19.131

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]
-0.15	-0.075		-0.15		0.486

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.601
r_dihedral_angle_6_deg	15.528
r_dihedral_angle_2_deg	10.318
r_lrange_it	6.666
r_scangle_it	6.516
r_scangle_other	6.514
r_lrange_other	6.462
r_dihedral_angle_1_deg	6.082
r_scbond_it	5.835
r_scbond_other	5.833
r_mcangle_it	3.943
r_mcangle_other	3.943
r_rigid_bond_restr	3.283
r_mcbond_it	3.106
r_mcbond_other	3.091
r_angle_refined_deg	1.3
r_angle_other_deg	0.445
r_symmetry_nbd_refined	0.335
r_nbd_refined	0.229
r_symmetry_nbd_other	0.189
r_symmetry_xyhbond_nbd_refined	0.188
r_nbd_other	0.187
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.154
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.065
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2302
Nucleic Acid Atoms
Solvent Atoms	151
Heterogen Atoms	42

Software

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