2JRR

Solution NMR Structure of Q5LLS5 from Silicibacter pomeroyi. Northeast Structural Genomics Consortium target SiR90

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-15N HSQC	0.65 mM 5% 13C, 100% 15N SiR90, 10 mM Tris, 5 mM DTT, 100 mM NaCl, 95% H2O/5% D2O		100	6.5	ambient	293
2	2D 1H-13C HSQC	0.65 mM 5% 13C, 100% 15N SiR90, 10 mM Tris, 5 mM DTT, 100 mM NaCl, 95% H2O/5% D2O		100	6.5	ambient	293
3	2D 1H-15N HSQC	0.65 mM [U-100% 13C; U-100% 15N] SiR90, 10 mM Tris, 5 mM DTT, 100 mM NaCl, 95% H2O/5% D2O		100	6.5	ambient	293
4	2D 1H-13C HSQC	0.65 mM [U-100% 13C; U-100% 15N] SiR90, 10 mM Tris, 5 mM DTT, 100 mM NaCl, 95% H2O/5% D2O		100	6.5	ambient	293
5	3D CBCA(CO)NH	0.65 mM [U-100% 13C; U-100% 15N] SiR90, 10 mM Tris, 5 mM DTT, 100 mM NaCl, 95% H2O/5% D2O		100	6.5	ambient	293
6	3D HNCACB	0.65 mM [U-100% 13C; U-100% 15N] SiR90, 10 mM Tris, 5 mM DTT, 100 mM NaCl, 95% H2O/5% D2O		100	6.5	ambient	293
7	3D HBHA(CO)NH	0.65 mM [U-100% 13C; U-100% 15N] SiR90, 10 mM Tris, 5 mM DTT, 100 mM NaCl, 95% H2O/5% D2O		100	6.5	ambient	293
8	3D HNHA	0.65 mM [U-100% 13C; U-100% 15N] SiR90, 10 mM Tris, 5 mM DTT, 100 mM NaCl, 95% H2O/5% D2O		100	6.5	ambient	293
9	3D HCCH-TOCSY	0.65 mM [U-100% 13C; U-100% 15N] SiR90, 10 mM Tris, 5 mM DTT, 100 mM NaCl, 95% H2O/5% D2O		100	6.5	ambient	293
10	3D 1H-15N NOESY	0.65 mM [U-100% 13C; U-100% 15N] SiR90, 10 mM Tris, 5 mM DTT, 100 mM NaCl, 95% H2O/5% D2O		100	6.5	ambient	293
11	3D 1H-13C NOESY	0.65 mM [U-100% 13C; U-100% 15N] SiR90, 10 mM Tris, 5 mM DTT, 100 mM NaCl, 95% H2O/5% D2O		100	6.5	ambient	293
12	2D 1H-15N HSQC	0.65 mM [U-100% 13C; U-100% 15N] SiR90, 10 mM Tris, 5 mM DTT, 100 mM NaCl, 100% D2O		100	6.5	ambient	293

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Varian	INOVA	600
2	Varian	INOVA	500

NMR Refinement
Method	Details	Software
simulated annealing	The structures are based on a total of 819 conformationally restricting NOE-derived distance constraints, 52 dihedral angle constraints, and 26 hydrogen bond constraints.(14.5 constraints per residue, 5.2 long-range constraints per residue, computed for residues 1-62 by PSVS 1.3). Residues 62-67 correspond to the Histidines of the C-terminal tag and could not be assigned. Structure determination was performed iteratively using AutoStructure (XPLOR-NIH). After a final XPLOR calculation using the constraints derived from AutoStructure, the 20 lowest energy structures out of 100 were further refined by restrained Molecular dynamics/Energy minimization in explicit water (CNS). The C-terminal HIS-tag residues of the protein were included in the calculations as well as the deposition. Coordinates for the following residues are not well determined: 1-7,18-29,46-48,58-67. The structure was determined using standard Triple resonance NMR experiments. Automated backbone assignments were made using AutoAssign and the sidechain assignments were completed manually. Automatic NOESY assignments as well as distance, dihedral angle and hydrogen-bond constraints were determined using AutoStructure. Structure quality factors, where ordered residues comprise: 8-17,30-45,49-57. RMSD of BB 0.5A, heavy atoms 1.0A. Ramachandran statistics for ordered residues: Most favoured: 91.1%, Additionally allowed: 8.9%, Generally allowed: 0.0%, Unfavourable: 0%. Procheck scores for ordered residues (raw/Z) phi-psi: -0.56/-1.89; all -0.33/-1.95. Molprobity clash score (raw/Z) 17.48/-1.47. RPF scores for goodness of fit to NOESY data: recall: 0.943, precision: 0.92, F-measure: 0.93. Final DP-score 0.795.	PSVS

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	100
Conformers Submitted Total Number	20
Representative Model	1 (lowest energy)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	structure validation	PSVS	1.3	Bhattacharya , Hang and Montelione
2	data analysis	PdbStat	4.1	Roberto Tejero and Montelione
3	refinement	CNS	1.1	Brunger, Adams, Clore, Gros, Nilges and Read
4	refinement	X-PLOR NIH	2.11.2	Schwieters, Kuszewski, Tjandra and Clore
5	refinement	AutoStructure	2.1.1	Huang, Tejero, Powers and Montelione
6	structure solution	AutoStructure	2.1.1	Huang, Tejero, Powers and Montelione
7	processing	NMRPipe	2.3	Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
8	data analysis	Sparky	3.110	Goddard
9	collection	VNMR	6.1c	Varian
10	chemical shift assignment	AutoAssign	2.2.1	Zimmerman, Moseley, Kulikowski and Montelione

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.