4P6Q | pdb_00004p6q

The crystal structure of the Split End protein SHARP adds a new layer of complexity to proteins containing RNA Recognition Motifs

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3MD1	Ensemble 1 (PDB codes: 3MD1, 2ADC, 2DNM, 2DGU, 2CQB); Ensemble 2 (PDB codes: X4AR, 2YTC, 4F26, 1WHY, 2CPZ); Ensemble 3 (PDB codes: 2I38, 1WHY, 1X55, 2LCW, 2CPE).
experimental model	PDB	2ADC	Ensemble 1 (PDB codes: 3MD1, 2ADC, 2DNM, 2DGU, 2CQB); Ensemble 2 (PDB codes: X4AR, 2YTC, 4F26, 1WHY, 2CPZ); Ensemble 3 (PDB codes: 2I38, 1WHY, 1X55, 2LCW, 2CPE).
experimental model	PDB	2DNM	Ensemble 1 (PDB codes: 3MD1, 2ADC, 2DNM, 2DGU, 2CQB); Ensemble 2 (PDB codes: X4AR, 2YTC, 4F26, 1WHY, 2CPZ); Ensemble 3 (PDB codes: 2I38, 1WHY, 1X55, 2LCW, 2CPE).
experimental model	PDB	2DGU	Ensemble 1 (PDB codes: 3MD1, 2ADC, 2DNM, 2DGU, 2CQB); Ensemble 2 (PDB codes: X4AR, 2YTC, 4F26, 1WHY, 2CPZ); Ensemble 3 (PDB codes: 2I38, 1WHY, 1X55, 2LCW, 2CPE).
experimental model	PDB	2CQB	Ensemble 1 (PDB codes: 3MD1, 2ADC, 2DNM, 2DGU, 2CQB); Ensemble 2 (PDB codes: X4AR, 2YTC, 4F26, 1WHY, 2CPZ); Ensemble 3 (PDB codes: 2I38, 1WHY, 1X55, 2LCW, 2CPE).
experimental model	PDB	2YTC	Ensemble 1 (PDB codes: 3MD1, 2ADC, 2DNM, 2DGU, 2CQB); Ensemble 2 (PDB codes: X4AR, 2YTC, 4F26, 1WHY, 2CPZ); Ensemble 3 (PDB codes: 2I38, 1WHY, 1X55, 2LCW, 2CPE).
experimental model	PDB	4F26	Ensemble 1 (PDB codes: 3MD1, 2ADC, 2DNM, 2DGU, 2CQB); Ensemble 2 (PDB codes: X4AR, 2YTC, 4F26, 1WHY, 2CPZ); Ensemble 3 (PDB codes: 2I38, 1WHY, 1X55, 2LCW, 2CPE).
experimental model	PDB	1WHY	Ensemble 1 (PDB codes: 3MD1, 2ADC, 2DNM, 2DGU, 2CQB); Ensemble 2 (PDB codes: X4AR, 2YTC, 4F26, 1WHY, 2CPZ); Ensemble 3 (PDB codes: 2I38, 1WHY, 1X55, 2LCW, 2CPE).
experimental model	PDB	2CPZ	Ensemble 1 (PDB codes: 3MD1, 2ADC, 2DNM, 2DGU, 2CQB); Ensemble 2 (PDB codes: X4AR, 2YTC, 4F26, 1WHY, 2CPZ); Ensemble 3 (PDB codes: 2I38, 1WHY, 1X55, 2LCW, 2CPE).
experimental model	PDB	2I38	Ensemble 1 (PDB codes: 3MD1, 2ADC, 2DNM, 2DGU, 2CQB); Ensemble 2 (PDB codes: X4AR, 2YTC, 4F26, 1WHY, 2CPZ); Ensemble 3 (PDB codes: 2I38, 1WHY, 1X55, 2LCW, 2CPE).
experimental model	PDB	1X55	Ensemble 1 (PDB codes: 3MD1, 2ADC, 2DNM, 2DGU, 2CQB); Ensemble 2 (PDB codes: X4AR, 2YTC, 4F26, 1WHY, 2CPZ); Ensemble 3 (PDB codes: 2I38, 1WHY, 1X55, 2LCW, 2CPE).
experimental model	PDB	2LCW	Ensemble 1 (PDB codes: 3MD1, 2ADC, 2DNM, 2DGU, 2CQB); Ensemble 2 (PDB codes: X4AR, 2YTC, 4F26, 1WHY, 2CPZ); Ensemble 3 (PDB codes: 2I38, 1WHY, 1X55, 2LCW, 2CPE).
experimental model	PDB	2CPE	Ensemble 1 (PDB codes: 3MD1, 2ADC, 2DNM, 2DGU, 2CQB); Ensemble 2 (PDB codes: X4AR, 2YTC, 4F26, 1WHY, 2CPZ); Ensemble 3 (PDB codes: 2I38, 1WHY, 1X55, 2LCW, 2CPE).

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	277	15% PEG 8000, 0.1M ammonium sulphate, 0.01M magnesium chloride, 0.05M 2-(N-morpholino)ethanesulfonic acid

Crystal Properties
Matthews coefficient	Solvent content
2.84	56.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.67	α = 90
b = 69.71	β = 90
c = 88.92	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 315r		2012-11-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM16	1.0	ESRF	BM16

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	2	28.71	99.67	20.44	5.38		26164

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	2		100			5.63

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	THROUGHOUT	Ensemble 1 (PDB codes: 3MD1, 2ADC, 2DNM, 2DGU, 2CQB); Ensemble 2 (PDB codes: X4AR, 2YTC, 4F26, 1WHY, 2CPZ); Ensemble 3 (PDB codes: 2I38, 1WHY, 1X55, 2LCW, 2CPE).	2	28.71	2	26035	1989	99.67	0.1959	0.1924	0.2	0.2377	0.23

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	15.497
f_angle_d	1.096
f_chiral_restr	0.081
f_bond_d	0.008
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2322
Nucleic Acid Atoms
Solvent Atoms	156
Heterogen Atoms	5

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	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.