8QRT | pdb_00008qrt

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8P8K

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIQUID DIFFUSION		293	17% (w/v) PEG4000, 23% 2-propanole, 100 mM tri sodium citrate trihydrate pH5,5

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.891	α = 90
b = 52.989	β = 91.665
c = 148.498	γ = 90

Symmetry
Space Group	P 1 21 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	PIXEL	Bruker PHOTON III		2021-08-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	BRUKER IMUS DIAMOND MICROFOCUS	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	20	90.6	0.076	11.2	3.2		77411

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.11			0.412

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	2	19.94	77410	3734	90.338	0.208	0.2063	0.21	0.2406	0.24	25.179

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]
-0.294		0.22	-0.609		0.889

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.191
r_dihedral_angle_4_deg	19.483
r_dihedral_angle_3_deg	15.948
r_dihedral_angle_1_deg	6.996
r_lrange_it	6.522
r_lrange_other	6.476
r_scangle_it	4.268
r_scangle_other	4.268
r_mcangle_it	3.296
r_mcangle_other	3.295
r_scbond_it	2.7
r_scbond_other	2.699
r_mcbond_it	2.146
r_mcbond_other	2.146
r_angle_refined_deg	1.479
r_angle_other_deg	1.258
r_nbd_refined	0.193
r_nbd_other	0.193
r_symmetry_nbd_other	0.191
r_xyhbond_nbd_refined	0.161
r_symmetry_nbd_refined	0.159
r_nbtor_refined	0.157
r_symmetry_xyhbond_nbd_refined	0.095
r_symmetry_nbtor_other	0.078
r_ncsr_local_group_6	0.071
r_ncsr_local_group_3	0.066
r_chiral_restr	0.065
r_ncsr_local_group_1	0.064
r_ncsr_local_group_4	0.064
r_symmetry_xyhbond_nbd_other	0.037
r_ncsr_local_group_2	0.033
r_ncsr_local_group_5	0.031
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8688
Nucleic Acid Atoms
Solvent Atoms	600
Heterogen Atoms	100

Software

Software
Software Name	Purpose
REFMAC	refinement
PROTEUM PLUS	data reduction
SCALA	data scaling
MOLREP	phasing