4V9R | pdb_00004v9r

Crystal structure of antibiotic DITYROMYCIN bound to 70S ribosome

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.6	292	0.1-0.2 M Arginine-HCl, 0.1M Tris-HCl pH 7.6, 2.5% PEG-20K, 7-12% MPD, 0.5mM BME, VAPOR DIFFUSION, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
3.32	58.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 210.08	α = 90
b = 449.83	β = 90
c = 619.65	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	DECTRIS PILATUS 6M-F	S/N 60-0112-F	2012-10-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.97900	APS	24-ID-C

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	49.748	98.8	0.199	0.236	6.19	3.45	1157340	1143138	1	-3	66.79

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	3.08	99.1		1.404	0.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	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	3	49.739	1.33	1142889	57314	98.78	0.2061	0.2033	0.2031	0.2586	0.2569	79.5902

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	17.113
f_angle_d	1.515
f_chiral_restr	0.062
f_bond_d	0.01
f_plane_restr	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	18671
Nucleic Acid Atoms	33933
Solvent Atoms	159
Heterogen Atoms	256

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction