6ESQ | pdb_00006esq

Structure of the acetoacetyl-CoA thiolase/HMG-CoA synthase complex from Methanothermococcus thermolithotrophicus soaked with acetyl-CoA

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	Crystallization was done under air using the sitting drop method (in a 24-well junior clover plate from Jena Bioscience). The crystallization reservoir contained 100 mM Tris/HCl pH 8.0, 25-28% v/v pentaerythritol ethoxylate (15/4 EO/OH, average Mn about 797) and 50 mM MgCl2. Crystallization drop contained 1 to 2 ul of the purified fraction containing Thiolase/HMGCS complex at 50-60 mg/ml (pure at 60%) and 1 ul of precipitant. The crystal was soaked in the crystallization condition supplemented 100 mM acetyl-CoA for 1 min 30 sec.

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.603	α = 90
b = 145.176	β = 90
c = 230.891	γ = 90

Symmetry
Space Group	P 21 21 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 PILATUS 6M		2016-06-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	1.64861	ESRF	ID23-1

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	2.95	49.3	99.4	0.143	0.04	0.999	14.9	13.3		76363			97.33

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	2.95	3.11	98.8		2.024	0.577	0.481	1.3	13.1

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.95	49.29	76299	3807	99.3	0.184	0.182	0.1901	0.23	0.2359	RANDOM	106.71

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]
1.0066			-15.6281		14.6215

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	15.01
t_omega_torsion	5.03
t_angle_deg	0.58
t_bond_d	0.005
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	26334
Nucleic Acid Atoms
Solvent Atoms	61
Heterogen Atoms	172

Software

Software
Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing