3PIP

Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2ZJR	PDB ENTRY 2ZJR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.

Crystal Properties
Matthews coefficient	Solvent content
4.4	72.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 169.723	α = 90
b = 408.562	β = 90
c = 693.334	γ = 90

Symmetry
Space Group	I 2 2 2

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	PSI PILATUS 6M			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA		SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	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	3.45	19.998	84.3	0.216	0.096	5.6	4.6		260194		0.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	3.45	3.57	85.6		1.4	4.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	ISOMORPHOUS REPLACEMENT	PDB ENTRY 2ZJR	3.45	19.998	0.58	260194	2635	83.3	0.257	0.257	0.301

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]
-20.514			6.816		-25.6717

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.358
f_angle_d	1.271
f_chiral_restr	0.067
f_bond_d	0.013
f_plane_restr	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	24479
Nucleic Acid Atoms	59311
Solvent Atoms
Heterogen Atoms	173

Software

Software
Software Name	Purpose
PHENIX	model building
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

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.