4V7S | pdb_00004v7s

Crystal structure of the E. coli ribosome bound to telithromycin.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3I1M	PDB ENTRY 3I1M, 3I1N, 3I1O, 3I1P
experimental model	PDB	3I1N	PDB ENTRY 3I1M, 3I1N, 3I1O, 3I1P
experimental model	PDB	3I1O	PDB ENTRY 3I1M, 3I1N, 3I1O, 3I1P
experimental model	PDB	3I1P	PDB ENTRY 3I1M, 3I1N, 3I1O, 3I1P

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	6.5	291	PEG8k, MPD, pH 6.5, microbatch, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.34	63.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 210.759	α = 90
b = 433.272	β = 90
c = 618.863	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			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.1	ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	3.25	100	91.2	0.083	15.2	2.5	801811	801811	2	2

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	3.25	3.31	81.1		0.455		1.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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	FOURIER SYNTHESIS	PDB ENTRY 3I1M, 3I1N, 3I1O, 3I1P	3.2547	85.218	0.02	754750	754750	15234	85.76	0.1943	0.1933	0.22	0.245	0.27

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]
-2.2555			-12.542		9.4561

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	19.323
f_angle_d	0.923
f_chiral_restr	0.063
f_bond_d	0.006
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	18554
Nucleic Acid Atoms	32895
Solvent Atoms	208
Heterogen Atoms	43

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHENIX	refinement

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.