NMR / X-Ray crystallography structure pair data archive.

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This archive is maintained by Gaetano Montelione (monteg3@rpi.edu)
Table 1. Data sets for 41 NESG NMR/X-Ray Pairs Determined by Conventional Triple-Resonance NMR Methods on Fully Protonated Samples

n NESG ID PDB ID Sequence Length Resolution(Å) Space group Coordinates Structure factor NMR PDB ID Sequence Molecule Coordinates Constraints BMRB ID Chemical Shift Peaks List FID RDC .
1 BeR31 3CPK 3CPK.seq 150 2.5 P43212 3CPK.pdb 3CPK-sf.cif 2K2E 2K2E.seq monomer 2K2E.pdb 2K2E.mr (grid) 15702 15702.bmrb NA NA Phage
2 CcR55 2O0Q 2O0Q.seq 115 1.8 C222 2O0Q.pdb 2O0Q-sf.cif 2JQN 2JQN.seq monomer 2JQN.pdb 2JQN.mr (grid) 15281 15281.bmrb 15281.peaks 15281.fid NA
3 CsR4 2OTA 2OTA.seq 76(2) 2.2 P212121 2OTA.pdb 2OTA-sf.cif 2JR2 2JR2.seq dimer 2JR2.pdb 2JR2.mr (grid) 15317 15317.bmrb 15317.peaks 15317.fid PEG PEG+CTAB Phage
4 CtR107 3E0H 3E0H.seq 158 1.81 P212121 3E0H.pdb 3E0H-sf.cif 2KCU 2KCU.seq monomer 2KCU.pdb 2KCU.mr (grid) 16097 16097.bmrb 16097.peaks 16097.fid PEG Phage
5 CtR148A 3IBW 3IBW.seq 88(2) 1.93 P43212 3IBW.pdb 3IBW-sf.cif 2KO1 2KO1.seq dimer 2KO1.pdb 2KO1.mr (grid) 16486 16486.bmrb 16486.peaks 16486.fid PAG PEG
6 DhR29B 3LYW 3LYW.seq 90 1.9 P43212 3LYW.pdb 3LYW-sf.cif 2KPU 2KPU.seq monomer 2KPU.pdb 2KPU.mr (grid) 16570 16570.bmrb 16570.peaks NA PAG PEG
7 DhR8C 3IPF 3IPF.seq 71(2) 1.99 P6122 3IPF.pdb 3IPF-sf.cif 2KYI 2KYI.seq dimer 2KYI.pdb 2KYI.mr (grid) 16656 16656.bmrb 16656.peaks NA PAG PEG
8 DrR147D 3GGN 3GGN.seq 155(2) 2.0 P1211 3GGN.pdb 3GGN-sf.cif 2KCZ 2KCZ.seq monomer 2KCZ.pdb 2KCZ.mr (grid) 16100 16100.bmrb 16100.peaks 16100.fid NA
9 ER382A 3FIF 3FIF.seq 61(8),7 2.7 P1 3FIF.pdb 3FIF-sf.cif 2JN0 2JN0.seq monomer 2JN0.pdb 2JN0.mr (grid) 15079 15079.bmrb NA NA NA
10 GmR137 3CWI 3CWI.seq 78 1.9 P43212 3CWI.pdb 3CWI-sf.cif 2K5P 2K5P.seq monomer 2K5P.pdb 2K5P.mr (grid) 15844 15844.bmrb 15844.peaks 15844.fid PEG Phage
11 HR1958 1TVG 1TVG.seq 153 1.6 C121 1TVG.pdb 1TVG-sf.cif 1XPW 1XPW.seq monomer 1XPW.pdb 1XPW.mr (grid) 6344 6344.bmrb 6344.peaks 6344.fid NA
12 HR3102A 3KW6 3KW6.seq 78 2.1 P3121 3KW6.pdb 3KW6-sf.cif 2KRK 2KRK.seq monomer 2KRK.pdb 2KRK.mr (grid) 16640 16640.bmrb 16640.peaks NA NA
13 HR3646E 3FIA 3FIA.seq 121 1.45 C121 3FIA.pdb 3FIA-sf.cif 2KHN 2KHN.seq monomer 2KHN.pdb 2KHN.mr (grid) 16250 16250.bmrb 16250.peaks 16250.fid PAG PEG
14 HR41 3EVX 3EVX.seq 175(4) 2.54 P1 3EVX.pdb 3EVX-sf.cif 2K07 2K07.seq monomer 2K07.pdb 2K07.mr (grid) 6546 6546.bmrb 6546.peaks 6546.fid NA
15 HR4435B 3NZL 3NZL.seq 83 1.2 P212121 3NZL.pdb 3NZL-sf.cif 2L1P 2L1P.seq monomer 2L1P.pdb 2L1P.mr (grid) 17092 17092.bmrb 17092.peaks NA PAG PEG
16 HR4527E 3P1X 3P1X.seq 75(2) 1.9 C2 3P1X.pdb 3P1X-sf.cif 2L33 2L33.seq monomer 2L33.pdb 2L33.mr (grid) 17169 17169.bmrb 17169.peaks 17169.fid PAG PEG
17 HR4694F 3NY5 3NY5.seq 96(4) 1.99 P212121 3NY5.pdb 3NY5-sf.cif 2L05 2L05.seq monomer 2L05.pdb 2L05.mr (grid) 17436 17436.bmrb 17436.peaks NA PEG
18 HR5546A 3JT0 3JT0.seq 144(2) 2.39 P212121 3JT0.pdb 3JT0-sf.cif 2KPW 2KPW.seq monomer 2KPW.pdb 2KPW.mr (grid) 16572 16572.bmrb 16572.peaks 16572.fid PAG PEG
19 LaR80A 3Q69 3Q69.seq 122 2.40 C121 3Q69.pdb 3Q69-sf.cif 2LFI 2LFI.seq monomer 2LFI.pdb 2LFI.mr (grid) 17754 17754.bmrb NA 17754.fid Phage Gel
20 LkR112 3LD7 3LD7.seq 101(3) 1.55 C2 3LD7.pdb 3LD7-sf.cif 2KPP 2KPP.seq monomer 2KPP.pdb 2KPP.mr (grid) 16563 16563.bmrb 16563.peaks NA PAG
21 MbR242E 3GW2 3GW2.seq 108 2.1 P6422 3GW2.pdb 3GW2-sf.cif 2KKO 2KKO.seq dimer 2KKO.pdb 2KKO.mr (grid) 16368 16368.bmrb 16368.peaks 16368.fid PAG PEG
22 MiR12 4FPW 4FPW.seq 181(2) 2.50 P61 4FPW.pdb 4FPW-sf.cif 2LUZ 2LUZ.seq dimer 2LUZ.pdb 2LUZ.mr (grid) 18547 18547.bmrb NA NA PEG Gel
23 MrR110B 3E0E 3E0E.seq 97 1.6 P212121 3E0E.pdb 3E0E-sf.cif 2K5V 2K5V.seq monomer 2K5V.pdb 2K5V.mr (grid) 15849 15849.bmrb 15849.peaks 15849.fid NA
24 OR8C 2RHK 2RHK.seq 140(2),72(2) 1.95 P41 2RHK.pdb 2RHK-sf.cif 2KKZ 2KKZ.seq monomer 2KKZ.pdb 2KKZ.mr (grid) 16376 16376.bmrb 16376.peaks 16376.fid NA
25 PfR193A 3IDU 3IDU.seq 127(2) 1.7 P1211 3IDU.pdb 3IDU-sf.cif 2KL6 2KL6.seq monomer 2KL6.pdb 2KL6.mr (grid) 16385 16385.bmrb 16385.peaks 16385.fid Phage
26 PsR293 3H9X 3H9X.seq 125(4) 2.51 P1 3H9X.pdb 3H9X-sf.cif 2KFP 2KFP.seq monomer 2KFP.pdb 2KFP.mr (grid) 16186 16186.bmrb 16186.peaks 16186.fid NA
27 RpR324 3LMO 3LMO.seq 101 2 P3211 3LMO.pdb 3LMO-sf.cif 2LPK 2LPK.seq monomer 2LPK.pdb 2LPK.mr (grid) 18263 18263.bmrb 18263.peaks NA PEG Phage
28 SPR104 3OBH 3OBH.seq 82(2) 1.89 P41 3OBH.pdb 3OBH-sf.cif 2L3A 2L3A.seq dimer 2L3A.pdb 2L3A.mr (grid) 17175 17175.bmrb 17175.peaks 17175.fid PAG PEG
29 SR213 2IM8 2IM8.seq 131(2) 2 P212121 2IM8.pdb 2IM8-sf.cif 2HFI 2HFI.seq monomer 2HFI.pdb 2HFI.mr (grid) 16113 16113.bmrb 16113.peaks 16113.fid NA
30 SR384 3BHP 3BHP.seq 60(3) 2.01 C121 3BHP.pdb 3BHP-sf.cif 2JVD 2JVD.seq monomer 2JVD.pdb 2JVD.mr (grid) 15476 15476.bmrb 15476.peaks 15476.fid NA
31 SR478 2GSV 2GSV.seq 80(2) 1.9 P121 2GSV.pdb 2GSV-sf.cif 2JS1 2JS1.seq dimer 2JS1.pdb 2JS1.mr (grid) 15350 15350.bmrb 15350.peaks 15350.fid NA
32 SgR209C 3OSJ 3OSJ.seq 147(4) 2.3 P21 3OSJ.pdb 3OSJ-sf.cif 2L06 2L06.seq monomer 2L06.pdb 2L06.mr (grid) 17031 17031.bmrb 17031.peaks 17031.fid PAG PEG
33 SgR42 3C4S 3C4S.seq 66(2) 1.7 P32 3C4S.pdb 3C4S-sf.cif 2JZ2 2JZ2.seq monomer 2JZ2.pdb 2JZ2.mr (grid) 15604 15604.bmrb 15604.peaks NA PEG
34 SoR77 2QTI 2QTI.seq 80 2.3 P43212 2QTI.pdb 2QTI-sf.cif 2JUW 2JUW.seq dimer 2JUW.pdb 2JUW.mr (grid) 15456 15456.bmrb 15456.peaks 15456.fid PAG
35 SrR115C 3MA5 3MA5.seq 100(4) 2.8 P6522 3MA5.pdb 3MA5-sf.cif 2KCV 2KCV.seq monomer 2KCV.pdb 2KCV.mr (grid) 16084 16084.bmrb 16084.peaks 16084.fid PEG Phage
36 SsR10 2Q00 2Q00.seq 129(2) 2.4 I4122 2Q00.pdb 2Q00-sf.cif 2JPU 2JPU.seq monomer 2JPU.pdb 2JPU.mr (grid) 15265 15265.bmrb 15265.peaks 15265.fid NA
37 StR65 2ES9 2ES9.seq 115 2 I213 2ES9.pdb 2ES9-sf.cif 2JN8 2JN8.seq monomer 2JN8.pdb 2JN8.mr (grid) 15089 15089.bmrb 15089.peaks 15089.fid NA
38 StR70 2ES7 2ES7.seq 142(4) 2.8 P1211 2ES7.pdb 2ES7-sf.cif 2JZT 2JZT.seq monomer 2JZT.pdb 2JZT.mr (grid) 7178 7178.bmrb NA NA NA
39 UuR17A 3K63 3K63.seq 126 2.49 P3211 3K63.pdb 3K63-sf.cif 2KRT 2KRT.seq monomer 2KRT.pdb 2KRT.mr (grid) 16648 16648.bmrb 16648.peaks 16648.fid NA
40 XcR50 1TTZ 1TTZ.seq 87 2.11 P65 1TTZ.pdb 1TTZ-sf.cif 1XPV 1XPV.seq monomer 1XPV.pdb 1XPV.mr (grid) 6363 6363.bmrb 6363.peaks NA NA
41 ZR18 2FFM 2FFM.seq 91 2.51 P41212 2FFM.pdb 2FFM-sf.cif 1PQX 1PQX.seq monomer 1PQX.pdb 1PQX.mr (grid) 5844 5844.bmrb NA 5844.fid NA





Table 2. Data Sets for 2H,13C,15N-ILV(CH3) Protein Samples 1
NMR X-Ray
n ID PDB ID Sequencea Length State Restraint BMRB ID CS file Peak Lists FID RDC c PDB ID Res. Space group Structure Factors
1 SgR145 (NESG) 2KW5 2KW5.seq 194 monomer 2KW5.mr (grid) 16806 16806.bmrb 16806.peaks 16806.fid P, Ph 3MER 2.2 P1 3MER.sf
2 HR4660B (NESG) 2LMD 2LMD.seq 163 monomer 2LMD.mr (grid) 18112 18112.bmrb 18112.peaks 18112.fid PAG - - - -
3 SR10 (NESG) 2KZN 2KZN.seq 143 monomer 2KZN.mr (grid) 17008 17008.bmrb 17008.peaks 17008.fid P, Ph, SG 3E0Oh 2.6 P3 3E0O.sf
4 WR73 (NESG) 2LOY 2LOY.seq 181 monomer 2LOY.mr (grid) 16833 16833.bmrb 16833.peaks 16833.fid Ph - - - -
5 HmR11 (NESG) 2LNU 2LNU.seq 182 monomer 2LNU.mr (grid) 18180 18180.bmrb 18180.peaks 18180.fid P, Ph - - - -
6 HsR50 (NESG) 2LOK 2LOK.seq 189 monomer 2LOK.mr (grid) 18215 18215.bmrb 18215.peaks 18215.fid P, Ph - - - -
7 ER690(NESG) [MBP] 2MV0 2MV0.seq 370 Complexb 2MV0.mr (grid) 25237 ER690.bmrb ER690.peaks ER690.fid 1EZP.mr (grid) 1DMBd,e 1.8 P1 1DMB.sf
8 BamC (non NESG) 2LAE d,f 2LAE.seq 246 monomer 2LAE.mr (grid) 17521 BamC.bmrb - - 1EZP.mr - - -
9 Rhodopsin (non NESG) 2KSY d,g 2KSY 247 Monomer 2KSY.mr (grid) 16678 16678.bmrb - - - 1H68d,g 2.1 C2221 1H68.sf

a. Total length of sequence at experimental conditions.
b. ER690 refers to the MBP/β-cyclodextrin complex.
c. P=PEG, Ph=Phage, SG=stretch Gel, PAG=Poly Acrylamide Gel.
d. Entries from previous work.
e. PDB ID: 1EZP and BMRB ID: 4986 Solution NMR structure with RDC (Ref: Muller & Kay 2000 J Mol. Biol. 300,197-212), PDB ID: 1DMB reference crystal structure(Ref: Sharff & Quiocho 1993 Biochemistry 32, 10553-10559).
f. PDB ID: 2LAE and BMRB ID: 17521 Solution NMR structure of BamC (Ref: Warner & Pardi 2011 J Mol. Biol. 411, 83-95).
g. PDB ID: 2KSY and BMRB ID:16678 Solution NMR Structure of Sensory Rhodopsin (Ref: Gautier & Nietlispach 2010 Nat. Struct. Mol Biol. 17, 768-774), PDB ID: 1H68Crystal structure of Sensory Rhodopsin (Ref: Royant & Navarro 2001 Proc Natl. Acad. Sci USA 98, 10131-10136).
h. PDB ID: 3E0O Crystal structure of MsrB (Ref: Kim &Hwang 2009 Mol. Microbiol. 72, 699-709).
1. Lange OF, Rossi P, Sgourakis N, Song Y, Lee HW, Aramini JM, Ertekin A, Xiao R, Acton TB, Montelione GT, Baker D (2012) The determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples. Proc. Natl. Acad. Sci. U.S.A. 109: 10873-10878.




Table 3. Results of Rosetta Refinement of 39 NESG NMR Structures 1

n Target Method Model# Coordinates Input filesa
1 BER31 R3Cons 20 link link
2 CCR55 R3Cons 20 link link
3 CSR4 R3Cons 20 link link
4 CTR107 R3Cons 20 link link
5 CTR148A R3Cons 20 link link
6 DHR29B R3Cons 20 link link
7 DHR8C R3Cons 20 link link
8 DRR147D R3Cons 18 link link
9 ER382A R3Cons 20 link link
10 GMR137 R3Cons 20 link link
11 HR1958 R3Cons 18 link link
12 HR3102A R3Cons 20 link link
13 HR3646E R3Cons 18 link link
14 HR41 R3Cons 20 link link
15 HR4435B R3Cons 20 link link
16 HR4527E R3Cons 20 link link
17 HR4694F R3Cons 20 link link
18 HR5546A R3Cons 20 link link
19 LKR112 R3Cons 20 link link
20 MBR242E R3Cons 18 link link
21 MRR110B R3Cons 20 link link
22 OR8C R3Cons 20 link link
23 PFR193A R3Cons 20 link link
24 PSR293 R3Cons 20 link link
25 RPR324 R3Cons 20 link link
26 SGR209C R3Cons 20 link link
27 SGR42 R3Cons 20 link link
28 SOR77 R3Cons 18 link link
29 SPR104 R3Cons 20 link link
30 SR213 R3Cons 20 link link
31 SR384 R3Cons 18 link link
32 SR478 R3Cons 20 link link
33 SRR115C R3Cons 20 link link
34 SSR10 R3Cons 20 link link
35 STR65 R3Cons 18 link link
36 STR70 R3Cons 20 link link
37 UUR17A R3Cons 20 link link
38 XCR50 R3Cons 20 link link
39 ZR18 R3Cons 10 link link

a. Input files including coordinate files, peak list files, chemical shift files and RPF control file.

1. Mao B, Tejero R, Baker D, Montelione GT (2014) Protein NMR structures refined with Rosetta have higher accuracy relative to corresponding X-Ray crystal structures.
   J. Amer. Chem. Soc. 2014, 136: 1893-1906.