4P6F | pdb_00004p6f

Crystal structure of the peptolide 12C bound to bacterial ribosome

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2WDG	2WDG, 2WDH, 2WDI, 2WDJ
experimental model	PDB	2WDH	2WDG, 2WDH, 2WDI, 2WDJ
experimental model	PDB	2WDI	2WDG, 2WDH, 2WDI, 2WDJ
experimental model	PDB	2WDJ	2WDG, 2WDH, 2WDI, 2WDJ

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	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	0.22	0.2542	0.25	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 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.