2L9H

Oligomeric Structure of the Chemokine CCL5/RANTES from NMR, MS, and SAXS Data

SOLUTION NMR - SOLUTION SCATTERING

Solution Scattering Data Acquistion	1
Scattering Type	x-ray
Radiation/Neutron Source	Bruker NanostarU TXS
Synchrotron	N
Beamline Type
Detector Type	AXS Vantec 2000
Detector Manufacturer Details	Bruker
Temperature (K)	288
pH	4.5
Numer of Time Frames Used	10
Protein Concentration Range (mg/mL)	7 - 10
Sample Buffer	ACETATE
Data Reduction Software	SAXS for Windows XP
Guiner Mean Radius Of Gyration (nm)	31
Sigma Mean Radius Of Gyration	0.01
R(XS-1) Mean Cross Sectional Radii (nm)
R(XS-1) Sigma Mean Cross Sectional Radii
R(XS-2) Mean Cross Sectional Radii (nm)
R(XS-2) Sigma Mean Cross Sectional Radii
P(R) Protein Length (nm)	121

Solution Scattering Data Analysis and Model Fitting
Method	Software	Software Authors	Starting Model	Conformers, Number Calculated	Conformers, Number Submitted	Conformers, Selection Criteria	Best Representative Conformer	Other Details
CONSTRAINED SCATTERING FITTING INCORPORATING NMR RDC DATA.	VMD, GNOM, OLIGOMER	UIUC, EMBL		5953	1	THE MODELS WERE GENERATED USING GRID SEARCH, CONTRAINING THE ORIENTATION BETWEEN THE DIMERS ACCORDING TO NMR RDC DATA. MODELS WERE THEN SCORED BASED ON AGREEMENT BETWEEN THEORETICAL AND EXPERIMENTAL SCATTERING CURVE AND SOUNDNESS OF THE INTERFACE AS DEFINED BY A RESIDUE PAIRING SCORE.	1	PDB CODE 1U4L

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-15N J-mod TROSY	1 mM [U-100% 15N] ccl5, 50 mM sodium acetate	90% H2O/10% D2O	0.05	4.4	ambient	297
2	2D 1H-15N TROSY	1 mM [U-100% 15N] ccl5, 50 mM sodium acetate, 5 % polyacrylamide	90% H2O/10% D2O	0.05	4.4	ambient	297
3	2D 1H-15N HSQC	1 mM [U-100% 15N] ccl5, 50 mM sodium acetate, 5 % polyacrylamide	90% H2O/10% D2O	0.05	4.4	ambient	297
4	2D 1H-15N J-mod TROSY	1 mM [U-100% 15N] ccl5, 50 mM sodium acetate, 5 % polyacrylamide	90% H2O/10% D2O	0.05	4.4	ambient	297
5	2D 1H-15N HSQC	1 mM [U-100% 15N] ccl5, 50 mM sodium acetate	90% H2O/10% D2O	0.05	4.4	ambient	297

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Varian	INOVA	800
2	Varian	INOVA	900

NMR Refinement
Method	Details	Software
molecular dynamics, SAXS-potential guided scoring within grid search		NAMD

NMR Ensemble Information
Conformer Selection Criteria	target function based on SAXS & knowledge-based potential
Conformers Calculated Total Number	1
Conformers Submitted Total Number	1
Representative Model	1 (best agreement with data)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	refinement	NAMD		Phillips, Braun, Wang, Gumbart, Tajkhorshid, Villa, Chipot, Skeel, Kale, and Schulte
2	data analysis	NMRView		Johnson, One Moon Scientific
3	collection	VNMRJ		Varian
4	refinement	VMD		Humphrey, Dalke & Schulten.

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.