4V97 | pdb_00004v97

Crystal structure of the bacterial ribosome ram mutation G299A.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2WDG	PDB ENTRIES 2WDG 2WDH 2WDI 2WDJ
experimental model	PDB	2WDH	PDB ENTRIES 2WDG 2WDH 2WDI 2WDJ
experimental model	PDB	2WDI	PDB ENTRIES 2WDG 2WDH 2WDI 2WDJ
experimental model	PDB	2WDJ	PDB ENTRIES 2WDG 2WDH 2WDI 2WDJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	4% PEG 20k, 4% PEG550 MME, 0.1M TRIS-ACETATE, 0.2M KSCN, 10mM MgCl2, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.53	61.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 210.459	α = 90
b = 447.344	β = 90
c = 622.298	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	mirrors	2011-07-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.9792	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	3.5	50	99.9	0.438	0.461	6.3	11.5	720970	720017	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.5	3.7	99.9		1.303	1.382	1.8	9.6

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	MOLECULAR REPLACEMENT	PDB ENTRIES 2WDG 2WDH 2WDI 2WDJ	3.516	35.071	1.99	720970	719893	32818	99.86	0.2119	0.2102	0.21	0.2493	0.25

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]
-9.4477			5.0433		5.6251

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	20.121
f_angle_d	1.052
f_chiral_restr	0.088
f_bond_d	0.009
f_plane_restr	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	19156
Nucleic Acid Atoms	36211
Solvent Atoms
Heterogen Atoms	501

Software

Software
Software Name	Purpose
ADSC	data collection
PHENIX	model building
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
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.