7S6B | pdb_00007s6b

Crystal structure of modular polyketide synthase apo-Lsd14 from the Lasalocid biosynthesis pathway, trapped in the transacylation step

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4	291	0.2 M lithium sulfate, 0.015 M magnesium sulfate, 0.1 M sodium acetate, pH 4.0, and 22% polyacrylic acid 5100

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.74	α = 99.63
b = 92.85	β = 94.93
c = 107.45	γ = 106.07

Symmetry
Space Group	P 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 PILATUS 6M		2018-05-02	M	SINGLE WAVELENGTH
2	1	x-ray	100	PIXEL	DECTRIS PILATUS3 6M		2018-03-15	M	SINGLE WAVELENGTH
3	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2018-02-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.9795	SSRL	BL9-2
2	SYNCHROTRON	ALS BEAMLINE 5.0.2	1.005	ALS	5.0.2
3	SYNCHROTRON	APS BEAMLINE 17-ID	1.000	APS	17-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.35	39.2	98.1	0.999	18.5	26.3		130003

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.35	2.41	94.2		0.683	1.3	15.2

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	SAD	THROUGHOUT	2.35	39.2	130003	6501	98.1	0.2076	0.2059	0.2	0.2411	0.24	RANDOM	77.77

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]
-13.2409	-10.5903	-0.0883	4.5691	-2.6495	8.6718

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	15.03
t_omega_torsion	2.77
t_angle_deg	0.89
t_bond_d	0.007
t_dihedral_angle_d
t_gen_planes
t_it
t_chiral_improper_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	21194
Nucleic Acid Atoms
Solvent Atoms	829
Heterogen Atoms

Software

Software
Software Name	Purpose
BUSTER	refinement
XDS	data reduction
autoPROC	data reduction
XDS	data scaling
autoPROC	data scaling
PHENIX	phasing
Coot	model building

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.