Experiment: 8VZK

Crystal Structure of 2-Hydroxyacyl-CoA Lyase/Synthase CfhHACS from Chloroflexi bacterium in the Complex with THDP and ADP

X-RAY DIFFRACTION

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, SITTING DROP	7.5	289	0.2 magnesium chloride, 0.1 M hepes pH 7.5, 30 % (v/v) PEG400

Crystal Properties
Matthews coefficient	Solvent content
2.87	57.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.327	α = 90
b = 111.327	β = 90
c = 193.164	γ = 120

Symmetry
Space Group	P 31 2 1

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 PILATUS3 X 6M		2022-12-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97918	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.65	50	97.1	0.162	0.168	1	13	14.2		39660			59.17

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.65	2.7	68.4		0.913	0.952	0.837	1	8.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.65	48.23	1.35	39475	1913	96.61	0.2134	0.2118	0.212	0.2444	0.2449	70.22

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	12.1755
f_angle_d	0.4849
f_chiral_restr	0.0424
f_plane_restr	0.0042
f_bond_d	0.0017

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8209
Nucleic Acid Atoms
Solvent Atoms	4
Heterogen Atoms	127

Software

Software
Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MOLREP	phasing