Experiment: 5IWA

Crystal structure of the 30S ribosomal subunit from Thermus thermophilus in complex with the GE81112 peptide antibiotic

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2ZM6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		292	HEPES-KOH, MgCl2, NH4Cl, beta-mercaptoethanol, MPD, spermidine

Crystal Properties
Matthews coefficient	Solvent content
4.85	74.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 413.14	α = 90
b = 413.14	β = 90
c = 173.63	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	90	PIXEL	PSI PILATUS 6M		2010-08-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.0000	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	3.5	160	99.9	0.165	9.79	11.3		187400		-3

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	3.5	3.69	99.6		2.379	1.46	11.6

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	2ZM6	3.5	80.034	1.33	187167	9368	99.81	0.1687	0.1661	0.1686	0.2177	0.2171	146.2449

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]
9.1813			9.1813		-18.3625

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	15.748
f_angle_d	1.175
f_chiral_restr	0.07
f_bond_d	0.023
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	19249
Nucleic Acid Atoms	32435
Solvent Atoms
Heterogen Atoms	251

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing
Coot	model building
PDB_EXTRACT	data extraction