9WNY | pdb_00009wny

EstS1 esterase active site mutant S154A in complex with Bis(2-hydroxyethyl) terephthalate (BHET)

X-RAY DIFFRACTION

---

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, SITTING DROP		293.15	Sodium malonate, 0.1 M HEPES (pH 7.0), Jeffamine ED-2001

Crystal Properties
Matthews coefficient	Solvent content
2.20869827	44.3456879

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.502	α = 90
b = 106.502	β = 90
c = 44.945	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		2025-01-22	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)	R Merge I (Observed)	Rpim 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	2	27.55	100	0.102	0.037	22.3	15.04		19907

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.05	100		0.369	0.925	6.9	11.2

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	22.482	19890	1008	99.91	0.181	0.1786	0.1787	0.2232	0.2235	12.487

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]
0.077	0.039		0.077		-0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.168
r_dihedral_angle_3_deg	14.317
r_dihedral_angle_2_deg	13.494
r_dihedral_angle_1_deg	6.357
r_lrange_it	6.019
r_scangle_it	3.549
r_scbond_it	2.247
r_mcangle_it	2.027
r_angle_refined_deg	1.853
r_mcbond_it	1.234
r_nbtor_refined	0.319
r_symmetry_nbd_refined	0.246
r_nbd_refined	0.236
r_symmetry_xyhbond_nbd_refined	0.217
r_xyhbond_nbd_refined	0.168
r_chiral_restr	0.12
r_gen_planes_refined	0.009
r_bond_refined_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2279
Nucleic Acid Atoms
Solvent Atoms	95
Heterogen Atoms	36

Software

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