4U52 | pdb_00004u52

Crystal structure of Nagilactone C bound to the yeast 80S ribosome

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3U5B	3U5B, 3U5C, 3U5D, 3U5E, 3U5F, 3U5G, 3U5H, 3U5I
experimental model	PDB	3U5C	3U5B, 3U5C, 3U5D, 3U5E, 3U5F, 3U5G, 3U5H, 3U5I
experimental model	PDB	3U5D	3U5B, 3U5C, 3U5D, 3U5E, 3U5F, 3U5G, 3U5H, 3U5I
experimental model	PDB	3U5E	3U5B, 3U5C, 3U5D, 3U5E, 3U5F, 3U5G, 3U5H, 3U5I
experimental model	PDB	3U5F	3U5B, 3U5C, 3U5D, 3U5E, 3U5F, 3U5G, 3U5H, 3U5I
experimental model	PDB	3U5G	3U5B, 3U5C, 3U5D, 3U5E, 3U5F, 3U5G, 3U5H, 3U5I
experimental model	PDB	3U5H	3U5B, 3U5C, 3U5D, 3U5E, 3U5F, 3U5G, 3U5H, 3U5I
experimental model	PDB	3U5I	3U5B, 3U5C, 3U5D, 3U5E, 3U5F, 3U5G, 3U5H, 3U5I

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	277	PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine

Crystal Properties
Matthews coefficient	Solvent content
3.04	59.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 435.39	α = 90
b = 286.22	β = 98.97
c = 303.33	γ = 90

Symmetry
Space Group	P 1 21 1

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		2013-07-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	1.0	SOLEIL	PROXIMA 1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	299.62	100	0.273	0.285	8.75	10.4		1459484		-3	66.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3	3.1	100		2.24	2.356	1.26

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3U5B, 3U5C, 3U5D, 3U5E, 3U5F, 3U5G, 3U5H, 3U5I	3	299.62	1459232	29182	99.97	0.2078	0.2068	0.2576	58.8982

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	19.08
f_angle_d	1.817
f_chiral_restr	0.071
f_bond_d	0.014
f_plane_restr	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	179692
Nucleic Acid Atoms	222116
Solvent Atoms
Heterogen Atoms	10978

Software

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