9WNZ | pdb_00009wnz

EstS1 esterase in complex with mono(2-hydroxyethyl) terephthalate (MHET) and Bis(2-hydroxyethyl) terephthalate (BHET)

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	100 mM HEPES pH 7.0, 0.5% v/v Jeffamine ED-2001, and 1.1 M sodium malonate

Crystal Properties
Matthews coefficient	Solvent content
2.21917367	44.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.748	α = 90
b = 106.748	β = 90
c = 44.95	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		2025-02-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54184

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	2.2	27.59	99.9	0.995	18.2	8.063		15070

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.27			0.953	8.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	AlphaFold	2.2	21.848	15059	770	99.861	0.2	0.1969	0.1975	0.2532	0.2543	12.231

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]
0.568	0.284		0.568		-1.842

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.665
r_dihedral_angle_6_deg	13.828
r_dihedral_angle_2_deg	8.384
r_dihedral_angle_1_deg	6.728
r_lrange_it	5.601
r_scangle_it	2.761
r_mcangle_it	2.038
r_angle_refined_deg	2.035
r_scbond_it	1.779
r_mcbond_it	1.228
r_nbtor_refined	0.321
r_symmetry_nbd_refined	0.293
r_nbd_refined	0.237
r_symmetry_xyhbond_nbd_refined	0.236
r_xyhbond_nbd_refined	0.194
r_chiral_restr	0.141
r_bond_refined_d	0.009
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2292
Nucleic Acid Atoms
Solvent Atoms	62
Heterogen Atoms	42

Software

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