2K50

Solution NMR Structure of the replication Factor A Related Protein from Methanobacterium thermoautotrophicum. Northeast Structural Genomics Target TR91A.

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-15N HSQC	1.25 mM [U-100% 13C; U-100% 15N] TR91A, 20 mM MES, 100 mM sodium chloride, 100 mM DTT, 5 mM Calcium Chloride, 0.02 % sodium azide	90% H2O/10% D2O	0.1	6.5	ambient	298
2	2D 1H-13C HSQC	1.25 mM [U-100% 13C; U-100% 15N] TR91A, 20 mM MES, 100 mM sodium chloride, 100 mM DTT, 5 mM Calcium Chloride, 0.02 % sodium azide	90% H2O/10% D2O	0.1	6.5	ambient	298
3	3D CBCA(CO)NH	1.25 mM [U-100% 13C; U-100% 15N] TR91A, 20 mM MES, 100 mM sodium chloride, 100 mM DTT, 5 mM Calcium Chloride, 0.02 % sodium azide	90% H2O/10% D2O	0.1	6.5	ambient	298
4	3D HNCACB	1.25 mM [U-100% 13C; U-100% 15N] TR91A, 20 mM MES, 100 mM sodium chloride, 100 mM DTT, 5 mM Calcium Chloride, 0.02 % sodium azide	90% H2O/10% D2O	0.1	6.5	ambient	298
5	3D HNCA	1.25 mM [U-100% 13C; U-100% 15N] TR91A, 20 mM MES, 100 mM sodium chloride, 100 mM DTT, 5 mM Calcium Chloride, 0.02 % sodium azide	90% H2O/10% D2O	0.1	6.5	ambient	298
6	3D HNCO	1.25 mM [U-100% 13C; U-100% 15N] TR91A, 20 mM MES, 100 mM sodium chloride, 100 mM DTT, 5 mM Calcium Chloride, 0.02 % sodium azide	90% H2O/10% D2O	0.1	6.5	ambient	298
7	3D HCCH-TOCSY	1.25 mM [U-100% 13C; U-100% 15N] TR91A, 20 mM MES, 100 mM sodium chloride, 100 mM DTT, 5 mM Calcium Chloride, 0.02 % sodium azide	90% H2O/10% D2O	0.1	6.5	ambient	298
8	3D HCCH-COSY	1.25 mM [U-100% 13C; U-100% 15N] TR91A, 20 mM MES, 100 mM sodium chloride, 100 mM DTT, 5 mM Calcium Chloride, 0.02 % sodium azide	90% H2O/10% D2O	0.1	6.5	ambient	298
9	3D CCH-TOCSY	1.25 mM [U-100% 13C; U-100% 15N] TR91A, 20 mM MES, 100 mM sodium chloride, 100 mM DTT, 5 mM Calcium Chloride, 0.02 % sodium azide	90% H2O/10% D2O	0.1	6.5	ambient	298
10	3D HBHA(CO)NH	1.25 mM [U-100% 13C; U-100% 15N] TR91A, 20 mM MES, 100 mM sodium chloride, 100 mM DTT, 5 mM Calcium Chloride, 0.02 % sodium azide	90% H2O/10% D2O	0.1	6.5	ambient	298
11	3D HN(CA)CO	1.25 mM [U-100% 13C; U-100% 15N] TR91A, 20 mM MES, 100 mM sodium chloride, 100 mM DTT, 5 mM Calcium Chloride, 0.02 % sodium azide	90% H2O/10% D2O	0.1	6.5	ambient	298
12	3D 1H-15N NOESY	1.25 mM [U-100% 13C; U-100% 15N] TR91A, 20 mM MES, 100 mM sodium chloride, 100 mM DTT, 5 mM Calcium Chloride, 0.02 % sodium azide	90% H2O/10% D2O	0.1	6.5	ambient	298
13	3D 1H-13C NOESY	1.25 mM [U-100% 13C; U-100% 15N] TR91A, 20 mM MES, 100 mM sodium chloride, 100 mM DTT, 5 mM Calcium Chloride, 0.02 % sodium azide	90% H2O/10% D2O	0.1	6.5	ambient	298
14	2D 1H-15N HSQC	1.33 mM U-100% 15N, 5 % 13C TR91A, 20 mM MES, 100 mM sodium chloride, 100 mM DTT, 5 mM Calcium Chloride, 0.02 % sodium azide	90% H2O/10% D2O	0.1	6.5	ambient	298
15	2D 1H-13C HSQC	1.33 mM U-100% 15N, 5 % 13C TR91A, 20 mM MES, 100 mM sodium chloride, 100 mM DTT, 5 mM Calcium Chloride, 0.02 % sodium azide	90% H2O/10% D2O	0.1	6.5	ambient	298
16	2D HET NOE	1.33 mM U-100% 15N, 5 % 13C TR91A, 20 mM MES, 100 mM sodium chloride, 100 mM DTT, 5 mM Calcium Chloride, 0.02 % sodium azide	90% H2O/10% D2O	0.1	6.5	ambient	298
17	Pseudo 2D T1	1.33 mM U-100% 15N, 5 % 13C TR91A, 20 mM MES, 100 mM sodium chloride, 100 mM DTT, 5 mM Calcium Chloride, 0.02 % sodium azide	90% H2O/10% D2O	0.1	6.5	ambient	298
18	Pseudo 2D T2 (CPMG)	1.33 mM U-100% 15N, 5 % 13C TR91A, 20 mM MES, 100 mM sodium chloride, 100 mM DTT, 5 mM Calcium Chloride, 0.02 % sodium azide	90% H2O/10% D2O	0.1	6.5	ambient	298

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE	600
2	Bruker	AVANCE	800

NMR Refinement
Method	Details	Software
torsion angle dynamics	To be used for REMARK 210: MONOMER BY GEL FILTRATION CHROMATOGRAPHY/LIGHT SCATTERING AND BY NMR. T1/T2 (MS) = 842.8/71.47, TAUC = 10.6(NS) CONSISTENT WITH MOLECULAR WEIGHT. STRUCTURE DETERMINED BY TRIPLE RESONANCE NMR SPECTROSCOPY. NOESY ASSIGNMENTS BY CYANA2.1. 20 OF 100 STRUCTURES LOWEST TARGET FUNCTION SELECTED WITH CYANA2.1. SELECTED MODELS ARE FURTHER REFINED USING CNS IN EXPLICIT WATER SHELL (NILGES PROTOCOL WITH PARAM19). ASSIGNMENT STATS (EXCLUDING C-TERM TAG): BACKBONE 94.53%, SIDECHAIN 88.01%, AROMATIC (SC) 95.83%, VL METHYL STEREOSPECIFIC 100%, UNAMBIGUOS SIDECHAIN NH2 100%. STRUCTURE BASED ON 1945 NOE, 214 DIHE. MAX NOE VIOLATION: 0.23 A (1MODEL); MAX DIHE VIOLATION: 6.9 DEG. 2 TOTAL CLOSE CONTACTS PER 20 MODELS. STRUCTURE QUALITY FACTOR (PSVS 1.3): ORDERED RESIDUES RANGES: 8-36, 40-84, 91-104 FOR [S(PHI)+S(PSI)] > 1.8. SECONDARY STRUCTURE - BETA STRANDS: (18-28, 32-33, 43-51, 54-61, 76-84, 93-96, 102-105). RMSD 0.4 BACKBONE, 0.8 ALL HEAVY ATOMS. RAMA. DISTRIBUTION: 91.3/8.6/0.1/0.0. PROCHECK (PSI-PHI): -0.61/-2.08 (RAW/Z), PROCHECK (ALL): -0.33/-1.95 (RAW/Z), MOLPROBITY CLASH: 18.22/-1.60 (RAW/Z). RPF SCORES ALL ASSIGNED RESIDUES (FIT OF NOESY PEAKLISTS TO STRUCTURE): RECALL: 0.93, PRECISION: 0.90, F-MEASURE: 0.92, DP-SCORE: 0.79.	CYANA

NMR Ensemble Information
Conformer Selection Criteria	target function
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 solution	CYANA	2.1	Guntert, Mumenthaler and Wuthrich
2	chemical shift assignment	AutoAssign	2.4.0	Zimmerman, Moseley, Kulikowski and Montelione
3	data analysis	Sparky	3.113	Goddard
4	processing	NMRPipe		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
5	geometry optimization	TALOS		Cornilescu, Delaglio and Bax
6	collection	TopSpin	2.1	Bruker Biospin
7	validation	PSVS		Bhattacharya and Montelione
8	validation	RPF(AutoStructure)		Huang, Tejero, Powers and Montelione
9	visualization	MOLMOL		Koradi, Billeter and Wuthrich
10	validation	Procheck		Laskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Tho
11	validation	MolProbity		Richardson
12	refinement	CNS	1.1	Brunger, Adams, Clore, Gros, Nilges and Read

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.