8P8K

Acyl-ACP thioesterase from Lemna paucicostata in complex with a thiazolopyridine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5X04

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		291	1.0 M sodium citrate tribasic, 100 mM MES pH 6.0

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.168	α = 90
b = 93.168	β = 90
c = 135.957	γ = 120

Symmetry
Space Group	P 32 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	OXFORD ONYX CCD		2020-12-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	OXFORD DIFFRACTION NOVA	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.8	23.13	98.9	0.102	0.993	9.9	3.5		17077

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	2.8	2.95			0.473	0.828

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	2.8	23.13	17072	864	98.183	0.223	0.2205	0.2775	38.818

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]
-0.204	-0.102		-0.204		0.662

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.197
r_dihedral_angle_3_deg	19.92
r_dihedral_angle_4_deg	19.584
r_lrange_it	8.685
r_lrange_other	8.684
r_dihedral_angle_1_deg	7.9
r_scangle_it	4.556
r_scangle_other	4.555
r_mcangle_it	4.526
r_mcangle_other	4.525
r_mcbond_it	2.721
r_mcbond_other	2.721
r_scbond_other	2.72
r_scbond_it	2.719
r_angle_refined_deg	1.535
r_angle_other_deg	1.314
r_nbd_other	0.229
r_nbd_refined	0.202
r_symmetry_nbd_other	0.197
r_symmetry_xyhbond_nbd_refined	0.195
r_nbtor_refined	0.167
r_xyhbond_nbd_refined	0.16
r_symmetry_nbd_refined	0.11
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.066
r_xyhbond_nbd_other	0.03
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4476
Nucleic Acid Atoms
Solvent Atoms	4
Heterogen Atoms	48

Software

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