4V9B | pdb_00004v9b

Crystal Structure of the 70S ribosome with tigecycline.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3UZ6	PDB ENTRY 3UZ6, 3UZ7, 3UZ8, 3UZ9
experimental model	PDB	3UZ7	PDB ENTRY 3UZ6, 3UZ7, 3UZ8, 3UZ9
experimental model	PDB	3UZ8	PDB ENTRY 3UZ6, 3UZ7, 3UZ8, 3UZ9
experimental model	PDB	3UZ9	PDB ENTRY 3UZ6, 3UZ7, 3UZ8, 3UZ9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	4% PEG20K, 4% PEGMME 550, 100mM Tris/HAc, 200mM KSCN, pH 7.5, vapor diffusion, hanging drop, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.3	62.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 210.06	α = 90
b = 450.27	β = 90
c = 616.89	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	PIXEL	PSI PILATUS 6M		2012-02-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.000	SLS	X06SA

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	3.1	300	99.9	0.466	10.46	44.5	1045946	1045188	-3	-3	96.184

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 (All)	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	MOLECULAR REPLACEMENT	PDB ENTRY 3UZ6, 3UZ7, 3UZ8, 3UZ9	3.1	153.588	1.34	1045946	1045138	2000	99.92	0.2136	0.2136	0.2135	0.21	0.2688	0.27	RANDOM	122.9958

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]
-14.3958			3.1805		11.2153

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	17.345
f_angle_d	1.015
f_chiral_restr	0.07
f_bond_d	0.008
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	19203
Nucleic Acid Atoms	35778
Solvent Atoms
Heterogen Atoms	966

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
RemDAq	data collection
PHENIX	model building
XDS	data reduction
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.