9QZ7 | pdb_00009qz7

Actinobacterial 2-hydroxyacyl-CoA lyase (AcHACL) mutant E493A 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	51.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.857	α = 90
b = 145.789	β = 90
c = 174.337	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	1.72	87.17	94	0.193	1	11.2	13.5		80334

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	1.72	1.89	71.8		1.908	0.6	1.6	12.9

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	1.72	87.168	80327	4076	57.499	0.164	0.1618	0.1618	0.2036	0.2036	26.507

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]
-0.319			0.56		-0.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.402
r_dihedral_angle_3_deg	12.275
r_dihedral_angle_1_deg	6.451
r_lrange_it	6.064
r_dihedral_angle_2_deg	5.415
r_scangle_it	3.502
r_scbond_it	2.368
r_mcangle_it	2.025
r_angle_refined_deg	1.617
r_mcbond_it	1.333
r_nbtor_refined	0.308
r_nbd_refined	0.209
r_symmetry_nbd_refined	0.193
r_symmetry_xyhbond_nbd_refined	0.177
r_xyhbond_nbd_refined	0.167
r_chiral_restr	0.104
r_ncsr_local_group_1	0.052
r_bond_refined_d	0.007
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8610
Nucleic Acid Atoms
Solvent Atoms	1043
Heterogen Atoms	165

Software

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