4V67 | pdb_00004v67

Crystal structure of a translation termination complex formed with release factor RF2.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3D5A	PDB ENTRIES 3D5A, 3D5B, 3D5C, 3D5D
experimental model	PDB	3D5B	PDB ENTRIES 3D5A, 3D5B, 3D5C, 3D5D
experimental model	PDB	3D5C	PDB ENTRIES 3D5A, 3D5B, 3D5C, 3D5D
experimental model	PDB	3D5D	PDB ENTRIES 3D5A, 3D5B, 3D5C, 3D5D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	296	100 MM TRIS-OAC, 200 MM KSCN, 3.5-4.5 % (W/V) PEG20K, 4-9 % PEG200, DEOXY BIGCHAP, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K

Crystal Properties
Matthews coefficient	Solvent content
3.45	64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 211.24	α = 90
b = 456.78	β = 90
c = 618.71	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	MARMOSAIC 300 mm CCD	SI(111) DOUBLE CRYSTAL MONOCHROMATOR. ADJUSTABLE FOCUSING MIRRORS IN K-B GEOMETRY	2008-04-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D		APS	23-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	49.951	97.9	8.8	16.8		1148216

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3	3.11	89.9		2.4	8.4

Refinement

Statistics
Diffraction ID	Structure Solution 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		PDB ENTRIES 3D5A, 3D5B, 3D5C, 3D5D	3	49.951	1.99	1148216	10481	97.34	0.2806	0.2803	0.27	0.3164	0.31

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]

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	21920
Nucleic Acid Atoms	35826
Solvent Atoms
Heterogen Atoms	528

Software

Software
Software Name	Purpose
PHENIX	refinement
CNS	refinement
XDS	data reduction
XDS	data scaling
CNS	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.