7PT2

Actinobacterial 2-hydroxyacyl-CoA lyase (AcHACL) mutant E493Q structure in complex with substrate 2-HIB-CoA and inactive cofactor 3-deaza-ThDP

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	25% PEG 1500, 0.1 M MIB buffer pH 7.0, 5 mM 3-deazathiamin diphosphate, 1 mM 2-Hydroxybutyryl-CoA, 5 mM MgCl2, 5 mM ADP

Crystal Properties
Matthews coefficient	Solvent content
2.51	51.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.674	α = 90
b = 145.481	β = 90
c = 174.198	γ = 90

Symmetry
Space Group	C 2 2 21

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	DECTRIS EIGER2 XE 16M		2021-07-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	1.762	87.099	95.4	0.103	0.031	0.999	15	11.9		83716

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.762	1.961	71.5		1.382	0.433	0.736	1.7	11.1

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	FOURIER SYNTHESIS	FREE R-VALUE	1.762	87.099	83716	4266	64.65	0.149	0.1466	0.1854	26.748

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]
-0.106			0.095		0.011

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.708
r_dihedral_angle_4_deg	19.203
r_dihedral_angle_3_deg	13.824
r_dihedral_angle_1_deg	6.848
r_lrange_it	5.142
r_lrange_other	4.978
r_scangle_it	3.057
r_scangle_other	3.057
r_scbond_it	1.989
r_scbond_other	1.988
r_angle_refined_deg	1.849
r_mcangle_it	1.844
r_mcangle_other	1.844
r_angle_other_deg	1.445
r_mcbond_it	1.229
r_mcbond_other	1.228
r_nbd_refined	0.21
r_xyhbond_nbd_refined	0.196
r_nbd_other	0.187
r_symmetry_nbd_other	0.182
r_symmetry_xyhbond_nbd_refined	0.175
r_symmetry_nbd_refined	0.162
r_nbtor_refined	0.158
r_symmetry_xyhbond_nbd_other	0.098
r_chiral_restr	0.09
r_symmetry_nbtor_other	0.086
r_ncsr_local_group_1	0.059
r_metal_ion_refined	0.025
r_bond_refined_d	0.014
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8602
Nucleic Acid Atoms
Solvent Atoms	1003
Heterogen Atoms	164

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
STARANISO	data scaling
MOLREP	phasing