4P6F

Crystal structure of the peptolide 12C bound to bacterial ribosome

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	3.5-4.5% PEG 20K, 3.5-4.5% PEG550 MME, 0.1M Tris-Acetate, 0.2M KSCN, 10 mM MgCl2
2	VAPOR DIFFUSION, SITTING DROP	7	293	3.5-4.5% PEG 20K, 3.5-4.5% PEG550 MME, 0.1M Tris-Acetate, 0.2M KSCN, 10 mM MgCl2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 209.24	α = 90
b = 443.46	β = 90
c = 618.62	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	CCD	ADSC QUANTUM 315		2010-12-06	M	SINGLE WAVELENGTH
2	1	100	CCD	ADSC QUANTUM 315		2010-12-06
3	2
4	2

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.9794	APS	24-ID-C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3.6	50	98	7.6	7.4		638335			91.29

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.6	3.7	95.8		1.169	1.8	6.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation 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	MOLECULAR REPLACEMENT	FREE R-VALUE	2WDG, 2WDH, 2WDI, 2WDJ	3.6	49.792	1.34	646099	29375	98.14	0.2237	0.2223	0.2542	79.9555

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	17.051
f_angle_d	0.887
f_chiral_restr	0.05
f_bond_d	0.006
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	93223
Nucleic Acid Atoms	201478
Solvent Atoms
Heterogen Atoms	786

Software

Software
Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.