9F7B | pdb_00009f7b

Thioesterase domain (GbnD6 TE domain) from the gladiolin PKS

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, HANGING DROP		293	22% PEG 8000 and 0.1 M CHES (pH 8.5).

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.745	α = 90
b = 60.009	β = 95.794
c = 63.472	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	293	PIXEL	DECTRIS EIGER X 16M		2021-07-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

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	43.5	99.94	0.1551	0.995	9.87	8.7		19199

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	99.97		0.6518	0.847	2.38	8.7

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	43.5	19199	946	99.974	0.174	0.1719	0.1817	0.2221	0.2271	21.962

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]
0.054		0.011	0.008		-0.063

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.496
r_dihedral_angle_3_deg	14.804
r_dihedral_angle_1_deg	6.785
r_dihedral_angle_2_deg	6.331
r_lrange_it	5.555
r_lrange_other	5.46
r_scangle_it	3.626
r_scangle_other	3.625
r_mcangle_other	3.121
r_mcangle_it	3.117
r_scbond_it	2.334
r_scbond_other	2.333
r_mcbond_it	1.979
r_mcbond_other	1.962
r_angle_refined_deg	1.341
r_angle_other_deg	0.446
r_nbd_refined	0.218
r_symmetry_xyhbond_nbd_refined	0.198
r_symmetry_nbd_refined	0.195
r_nbd_other	0.192
r_symmetry_nbd_other	0.188
r_nbtor_refined	0.181
r_xyhbond_nbd_refined	0.15
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.063
r_gen_planes_refined	0.007
r_bond_refined_d	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2275
Nucleic Acid Atoms
Solvent Atoms	173
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
DIALS	data scaling
PHASER	phasing