9J58 | pdb_00009j58

ESTS1 phthalate ester degrading esterase from Sulfobacillus acidophilus in complex with jeffamine

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	45.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.078	α = 90
b = 108.078	β = 90
c = 44.51	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		2022-08-05	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	27.69	100	0.05	27	2.95		47748

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	99.8		0.655	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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.5	25.973	47733	2361	99.964	0.119	0.117	0.1177	0.1633	0.1643	16.006

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]
0.505	0.253		0.505		-1.638

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.098
r_dihedral_angle_3_deg	14.185
r_dihedral_angle_2_deg	7.761
r_rigid_bond_restr	6.607
r_scangle_it	6.157
r_scangle_other	6.155
r_dihedral_angle_1_deg	6.071
r_scbond_it	5.966
r_scbond_other	5.964
r_lrange_it	5.007
r_lrange_other	5
r_mcangle_other	3.03
r_mcangle_it	3.025
r_mcbond_it	2.509
r_mcbond_other	2.509
r_angle_refined_deg	1.511
r_angle_other_deg	0.513
r_nbd_refined	0.231
r_symmetry_nbd_refined	0.207
r_symmetry_xyhbond_nbd_refined	0.186
r_symmetry_nbd_other	0.185
r_nbtor_refined	0.18
r_nbd_other	0.177
r_xyhbond_nbd_refined	0.173
r_chiral_restr	0.078
r_symmetry_nbtor_other	0.078
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2302
Nucleic Acid Atoms
Solvent Atoms	218
Heterogen Atoms	82

Software

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