7PT1 | pdb_00007pt1

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4RJI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	25% PEG 1500, 0.1 M MIB buffer (sodium malonate dibasic monohydrate, imidazole, boric acid) pH 6.0 5 mM 3-deazathiamin diphosphate, 1 mM 2-Hydroxyisobutyryl-CoA, 5 mM MgCl2, 5 mM ADP

Crystal Properties
Matthews coefficient	Solvent content
2.64	53.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.95	α = 90
b = 146.138	β = 90
c = 174.749	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		2021-07-15	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	1.553	87.374	89.4	0.114	0.035	0.999	10.1	11.4		100209

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	1.553	1.752	60.9		1.537	0.473	0.644	1.9

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	4RJI	1.553	87.374	100208	5011	52.676	0.161	0.1595	0.17	0.1936	0.2	20.939

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]
-0.347			0.443		-0.095

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.944
r_dihedral_angle_4_deg	18.798
r_dihedral_angle_3_deg	13.156
r_dihedral_angle_1_deg	6.879
r_lrange_it	4.685
r_lrange_other	4.494
r_scangle_it	2.96
r_scangle_other	2.96
r_scbond_it	1.944
r_scbond_other	1.944
r_mcangle_other	1.891
r_mcangle_it	1.89
r_angle_refined_deg	1.853
r_angle_other_deg	1.514
r_mcbond_it	1.257
r_mcbond_other	1.255
r_nbd_refined	0.218
r_symmetry_nbd_refined	0.217
r_symmetry_xyhbond_nbd_refined	0.193
r_nbd_other	0.187
r_symmetry_nbd_other	0.181
r_xyhbond_nbd_refined	0.173
r_nbtor_refined	0.163
r_symmetry_xyhbond_nbd_other	0.12
r_chiral_restr	0.095
r_symmetry_nbtor_other	0.084
r_ncsr_local_group_1	0.059
r_xyhbond_nbd_other	0.043
r_metal_ion_refined	0.017
r_bond_refined_d	0.014
r_gen_planes_refined	0.011
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	1017
Heterogen Atoms	163

Software

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