9QZ6 | pdb_00009qz6

Actinobacterial 2-hydroxyacyl-CoA lyase (AcHACL) structure in complex with 2-methylglyceryl-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	7PT1

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.768	α = 90
b = 146.493	β = 90
c = 174.321	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		2022-05-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9762	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	1.551	84.68	92.3	0.102	1	18.7	13.8		104204

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.551	1.694	72.2		1.682	0.64	1.6	13.3

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	1.551	84.68	104204	5203	54.642	0.159	0.1577	0.1576	0.1841	0.1842	22.955

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]
-0.064			0.139		-0.075

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.146
r_dihedral_angle_3_deg	11.765
r_dihedral_angle_1_deg	6.397
r_dihedral_angle_2_deg	6.048
r_lrange_it	5.91
r_scangle_it	3.607
r_scbond_it	2.444
r_mcangle_it	1.87
r_angle_refined_deg	1.789
r_mcbond_it	1.269
r_nbtor_refined	0.309
r_nbd_refined	0.208
r_symmetry_nbd_refined	0.193
r_xyhbond_nbd_refined	0.165
r_symmetry_xyhbond_nbd_refined	0.162
r_chiral_restr	0.113
r_ncsr_local_group_1	0.053
r_bond_refined_d	0.009
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8618
Nucleic Acid Atoms
Solvent Atoms	1065
Heterogen Atoms	165

Software

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