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- PDB-5tgm: Crystal structure of the S.cerevisiae 80S ribosome in complex wit... -

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Entry
Database: PDB / ID: 5tgm
TitleCrystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCA-Pro
Components
  • (18S ribosomal ...) x 2
  • (25S ribosomal ...) x 2
  • (40S Ribosomal Protein ...) x 31
  • (60S Ribosomal Protein ...) x 45
  • (ES17) x 2
  • (Guanine nucleotide-binding protein subunit beta-like ...) x 2
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • Peptidyl-tRNA analog ACCA-Leu-Phe
  • Ribosome-bound protein Stm1,Suppressor protein STM1,Ribosome-bound protein Stm1
  • Suppressor protein STM1,Ribosome-bound protein Stm1Silencer (firearms)
  • Ubiquitin-40S ribosomal protein S31
  • Ubiquitin-60S ribosomal protein L40
KeywordsRIBOSOME / ribosome / translation / protein synthesis / proline / aminoacyl-tRNA / peptide bond formation / catalysis / cyclic amino acids
Function / homologyRibosomal protein S7 domain superfamily / Ribosomal protein L7/L30 / Ribosomal protein L5 / Ribosomal protein L23 / Ribosomal protein S14p/S29e / Ribosomal protein L16p/L10e / Ubiquitin family / Ribosomal protein L14p/L23e / Ribosomal protein L22p/L17e / Ribosomal protein S19 ...Ribosomal protein S7 domain superfamily / Ribosomal protein L7/L30 / Ribosomal protein L5 / Ribosomal protein L23 / Ribosomal protein S14p/S29e / Ribosomal protein L16p/L10e / Ubiquitin family / Ribosomal protein L14p/L23e / Ribosomal protein L22p/L17e / Ribosomal protein S19 / Ribosomal protein S3, C-terminal domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein S7p/S5e / Ribosomal protein S12/S23 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein L14 / Ribosomal protein S15 / 60S ribosomal protein L19 / Ribosomal protein L30/YlxQ / Ribosomal protein L35A superfamily / Ribosomal protein L27e superfamily / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L40e superfamily / S27a-like superfamily / Ribosomal protein S21e superfamily / Ribosomal protein L34Ae superfamily / Ribosomal protein S26e superfamily / Ribosomal protein L22e superfamily / Ribosomal protein L7A/L8 superfamily / Ribosomal protein L38e superfamily / Ribosomal protein L3 / Ribosomal protein S2 / Ribosomal protein S19e domain superfamily / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal protein L31e / Ribosomal protein L6e / Ribosomal protein L36e / Ribosomal protein L21e / Ribosomal protein S6e / Ribosomal protein S19e / Ribosomal L40e family / Ribosomal S3Ae family / Ribosomal protein L44 / Ribosomal family S4e / Ribosomal S17 / Ribosomal L39 protein / Ribosomal L29 protein / Ribosomal L15 / Ribosomal protein L30p/L7e / ribosomal L5P family C-terminus / Ribosomal protein L4/L1 family / Ribosomal protein L13 / KOW motif / Ribosomal protein S13/S18 / Ribosomal protein S11 / Ribosomal protein S8 / WD domain, G-beta repeat / Ribosomal protein S9/S16 / Ribosomal protein S17 / Ribosomal protein L6 / Ribosomal protein S10p/S20e / Ribosomal protein S5, N-terminal domain / Ribosomal protein S4e, central domain superfamily / Ribosomal protein L36e domain superfamily / Ribosomal protein S28e / Ribosomal protein L4 domain superfamily / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S2, eukaryotic / Ribosomal protein S10 domain / 30s ribosomal protein S13, C-terminal / 60S ribosomal protein L4, C-terminal domain / Ribosomal protein L5 eukaryotic/L18 archaeal, C-terminal / Ribosomal protein L15e core domain superfamily / Ribosomal protein S7 domain / Ribosomal protein L19/L19e conserved site / Ribosomal protein L39e domain superfamily / Ribosomal protein L31e domain superfamily / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S19, superfamily / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein S28e conserved site / Ribosomal protein L13, conserved site / Ribosomal protein L24e, conserved site / Ribosomal protein L30, central domain, archaeal type / Ribosomal protein S15P / Ribosomal protein L30e, conserved site / Ribosomal protein L5 domain superfamily / Ribosomal protein S4/S9 / Ribosomal protein L2, conserved site / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein S8e/ribosomal biogenesis NSA2 / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L18e, conserved site / Ribosomal protein S17, archaeal/eukaryotic / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / 40S Ribosomal protein S10 / Winged helix-like DNA-binding domain superfamily / RNA-binding S4 domain superfamily / Ribosomal protein S11 superfamily
Function and homology information
Specimen sourceSaccharomyces cerevisiae (baker's yeast)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / 3.5 Å resolution
AuthorsMelnikov, S. / Mailliot, J. / Yusupov, M.
CitationJournal: EMBO Rep. / Year: 2016
Title: Molecular insights into protein synthesis with proline residues.
Authors: Melnikov, S. / Mailliot, J. / Rigger, L. / Neuner, S. / Shin, B.S. / Yusupova, G. / Dever, T.E. / Micura, R. / Yusupov, M.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 28, 2016 / Release: Jan 18, 2017
RevisionDateData content typeGroupProviderType
1.0Jan 18, 2017Structure modelrepositoryInitial release
1.1Jan 25, 2017Structure modelDerived calculations / Source and taxonomy / Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
2: 18S ribosomal RNA
S0: 40S ribosomal protein S0-A
S1: 40S ribosomal protein S1-A
S2: 40S ribosomal protein S2
S3: 40S ribosomal protein S3
S4: 40S ribosomal protein S4-A
S5: 40S ribosomal protein S5
S6: 40S ribosomal protein S6-A
S7: 40S ribosomal protein S7-A
S8: 40S ribosomal protein S8
S9: 40S ribosomal protein S9-A
C0: 40S ribosomal protein S10-A,40S Ribosomal Protein S10
C1: 40S ribosomal protein S11-A,40S Ribosomal Protein S11
C2: 40S Ribosomal Protein S12,40S ribosomal protein S12
C3: 40S ribosomal protein S13
C4: 40S ribosomal protein S14-A
C5: 40S Ribosomal Protein S15,40S ribosomal protein S15,40S Ribosomal Protein S15
C6: 40S ribosomal protein S16-A
C7: ES17
C8: 40S ribosomal protein S18-A
C9: 40S ribosomal protein S19-A
D0: 40S ribosomal protein S20
D1: 40S ribosomal protein S21-A
D2: 40S ribosomal protein S22-A
D3: 40S ribosomal protein S23-A
D4: 40S ribosomal protein S24-A
D5: 40S ribosomal protein S25-A
D6: 40S ribosomal protein S26-B
D7: 40S ribosomal protein S27-A
D8: 40S ribosomal protein S28-A
D9: 40S ribosomal protein S29-A
E0: 40S ribosomal protein S30-A
E1: Ubiquitin-40S ribosomal protein S31
SR: Guanine nucleotide-binding protein subunit beta-like protein
SM: Ribosome-bound protein Stm1,Suppressor protein STM1,Ribosome-bound protein Stm1
1: 25S ribosomal RNA
3: 5S ribosomal RNA
4: 5.8S ribosomal RNA
L2: 60S ribosomal protein L2-A
L3: 60S ribosomal protein L3
L4: 60S ribosomal protein L4-A
L5: 60S ribosomal protein L5
L6: 60S ribosomal protein L6-A
L7: 60S ribosomal protein L7-A
L8: 60S ribosomal protein L8-A
L9: 60S ribosomal protein L9-A
M0: 60S ribosomal protein L10
M1: 60S ribosomal protein L11-B
M3: 60S ribosomal protein L13-A
M4: 60S ribosomal protein L14-A
M5: 60S ribosomal protein L15-A
M6: 60S ribosomal protein L16-A
M7: 60S ribosomal protein L17-A
M8: 60S ribosomal protein L18-A
M9: 60S ribosomal protein L19-A
N0: 60S ribosomal protein L20-A
N1: 60S ribosomal protein L21-A
N2: 60S ribosomal protein L22-A
N3: 60S ribosomal protein L23-A
N4: 60S ribosomal protein L24-A
N5: 60S ribosomal protein L25
N6: 60S ribosomal protein L26-A
N7: 60S ribosomal protein L27-A
N8: 60S ribosomal protein L28
N9: 60S ribosomal protein L29
O0: 60S ribosomal protein L30
O1: 60S ribosomal protein L31-A
O2: 60S ribosomal protein L32
O3: 60S ribosomal protein L33-A
O4: 60S ribosomal protein L34-A
O5: 60S ribosomal protein L35-A
O6: 60S ribosomal protein L36-A
O7: 60S ribosomal protein L37-A
O8: 60S ribosomal protein L38
O9: 60S ribosomal protein L39
Q0: Ubiquitin-60S ribosomal protein L40
Q1: 60S ribosomal protein L41-A
Q2: 60S ribosomal protein L42-A
Q3: 60S ribosomal protein L43-A
6: 18S ribosomal RNA
s0: 40S ribosomal protein S0-A
s1: 40S ribosomal protein S1-A
s2: 40S ribosomal protein S2
s3: 40S ribosomal protein S3
s4: 40S ribosomal protein S4-A
s5: 40S ribosomal protein S5
s6: 40S ribosomal protein S6-A
s7: 40S ribosomal protein S7-A
s8: 40S ribosomal protein S8
s9: 40S ribosomal protein S9-A
c0: 40S ribosomal protein S10-A,40S Ribosomal Protein S10
c1: 40S ribosomal protein S11-A,40S Ribosomal Protein S11
c2: 40S Ribosomal Protein S12,40S ribosomal protein S12
c3: 40S ribosomal protein S13
c4: 40S ribosomal protein S14-A
c5: 40S Ribosomal Protein S15,40S ribosomal protein S15,40S Ribosomal Protein S15
c6: 40S ribosomal protein S16-A
c7: ES17
c8: 40S ribosomal protein S18-A
c9: 40S ribosomal protein S19-A
d0: 40S ribosomal protein S20
d1: 40S ribosomal protein S21-A
d2: 40S ribosomal protein S22-A
d3: 40S ribosomal protein S23-A
d4: 40S ribosomal protein S24-A
d5: 40S ribosomal protein S25-A
d6: 40S ribosomal protein S26-B
d7: 40S ribosomal protein S27-A
d8: 40S ribosomal protein S28-A
d9: 40S ribosomal protein S29-A
e0: 40S ribosomal protein S30-A
e1: Ubiquitin-40S ribosomal protein S31
sR: Guanine nucleotide-binding protein subunit beta-like protein
sM: Suppressor protein STM1,Ribosome-bound protein Stm1
5: 25S ribosomal RNA
7: 5S ribosomal RNA
8: 5.8S ribosomal RNA
l2: 60S ribosomal protein L2-A
l3: 60S ribosomal protein L3
l4: 60S ribosomal protein L4-A
l5: 60S ribosomal protein L5
l6: 60S ribosomal protein L6-A
l7: 60S ribosomal protein L7-A
l8: 60S ribosomal protein L8-A,60S Ribosomal Protein L8
l9: 60S ribosomal protein L9-A
m0: 60S ribosomal protein L10
m1: 60S ribosomal protein L11-B
m2: 60S Ribosomal Protein L12
m3: 60S ribosomal protein L13-A
m4: 60S ribosomal protein L14-A
m5: 60S ribosomal protein L15-A
m6: 60S ribosomal protein L16-A
m7: 60S ribosomal protein L17-A
m8: 60S ribosomal protein L18-A
m9: 60S ribosomal protein L19-A
n0: 60S ribosomal protein L20-A
n1: 60S ribosomal protein L21-A
n2: 60S ribosomal protein L22-A
n3: 60S ribosomal protein L23-A
n4: 60S ribosomal protein L24-A
n5: 60S ribosomal protein L25
n6: 60S ribosomal protein L26-A
n7: 60S ribosomal protein L27-A
n8: 60S ribosomal protein L28
n9: 60S ribosomal protein L29
o0: 60S ribosomal protein L30
o1: 60S ribosomal protein L31-A
o2: 60S ribosomal protein L32
o3: 60S ribosomal protein L33-A
o4: 60S ribosomal protein L34-A
o5: 60S ribosomal protein L35-A
o6: 60S ribosomal protein L36-A
o7: 60S ribosomal protein L37-A
o8: 60S ribosomal protein L38
o9: 60S ribosomal protein L39
q0: Ubiquitin-60S ribosomal protein L40
q1: 60S ribosomal protein L41-A
q2: 60S ribosomal protein L42-A
q3: 60S ribosomal protein L43-A
p0: 60S Ribosomal Protein P0
p1: 60S Ribosomal Protein P1/2
p2: 60S Ribosomal Protein P1/2
P: Peptidyl-tRNA analog ACCA-Leu-Phe
p: Peptidyl-tRNA analog ACCA-Leu-Phe
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,310,0172474
Polyers5,964,446164
Non-polymers345,5722310
Water0
1
6: 18S ribosomal RNA
s0: 40S ribosomal protein S0-A
s1: 40S ribosomal protein S1-A
s2: 40S ribosomal protein S2
s3: 40S ribosomal protein S3
s4: 40S ribosomal protein S4-A
s5: 40S ribosomal protein S5
s6: 40S ribosomal protein S6-A
s7: 40S ribosomal protein S7-A
s8: 40S ribosomal protein S8
s9: 40S ribosomal protein S9-A
c0: 40S ribosomal protein S10-A,40S Ribosomal Protein S10
c1: 40S ribosomal protein S11-A,40S Ribosomal Protein S11
c2: 40S Ribosomal Protein S12,40S ribosomal protein S12
c3: 40S ribosomal protein S13
c4: 40S ribosomal protein S14-A
c5: 40S Ribosomal Protein S15,40S ribosomal protein S15,40S Ribosomal Protein S15
c6: 40S ribosomal protein S16-A
c7: ES17
c8: 40S ribosomal protein S18-A
c9: 40S ribosomal protein S19-A
d0: 40S ribosomal protein S20
d1: 40S ribosomal protein S21-A
d2: 40S ribosomal protein S22-A
d3: 40S ribosomal protein S23-A
d4: 40S ribosomal protein S24-A
d5: 40S ribosomal protein S25-A
d6: 40S ribosomal protein S26-B
d7: 40S ribosomal protein S27-A
d8: 40S ribosomal protein S28-A
d9: 40S ribosomal protein S29-A
e0: 40S ribosomal protein S30-A
e1: Ubiquitin-40S ribosomal protein S31
sR: Guanine nucleotide-binding protein subunit beta-like protein
sM: Suppressor protein STM1,Ribosome-bound protein Stm1
5: 25S ribosomal RNA
7: 5S ribosomal RNA
8: 5.8S ribosomal RNA
l2: 60S ribosomal protein L2-A
l3: 60S ribosomal protein L3
l4: 60S ribosomal protein L4-A
l5: 60S ribosomal protein L5
l6: 60S ribosomal protein L6-A
l7: 60S ribosomal protein L7-A
l8: 60S ribosomal protein L8-A,60S Ribosomal Protein L8
l9: 60S ribosomal protein L9-A
m0: 60S ribosomal protein L10
m1: 60S ribosomal protein L11-B
m2: 60S Ribosomal Protein L12
m3: 60S ribosomal protein L13-A
m4: 60S ribosomal protein L14-A
m5: 60S ribosomal protein L15-A
m6: 60S ribosomal protein L16-A
m7: 60S ribosomal protein L17-A
m8: 60S ribosomal protein L18-A
m9: 60S ribosomal protein L19-A
n0: 60S ribosomal protein L20-A
n1: 60S ribosomal protein L21-A
n2: 60S ribosomal protein L22-A
n3: 60S ribosomal protein L23-A
n4: 60S ribosomal protein L24-A
n5: 60S ribosomal protein L25
n6: 60S ribosomal protein L26-A
n7: 60S ribosomal protein L27-A
n8: 60S ribosomal protein L28
n9: 60S ribosomal protein L29
o0: 60S ribosomal protein L30
o1: 60S ribosomal protein L31-A
o2: 60S ribosomal protein L32
o3: 60S ribosomal protein L33-A
o4: 60S ribosomal protein L34-A
o5: 60S ribosomal protein L35-A
o6: 60S ribosomal protein L36-A
o7: 60S ribosomal protein L37-A
o8: 60S ribosomal protein L38
o9: 60S ribosomal protein L39
q0: Ubiquitin-60S ribosomal protein L40
q1: 60S ribosomal protein L41-A
q2: 60S ribosomal protein L42-A
q3: 60S ribosomal protein L43-A
p0: 60S Ribosomal Protein P0
p1: 60S Ribosomal Protein P1/2
p2: 60S Ribosomal Protein P1/2
p: Peptidyl-tRNA analog ACCA-Leu-Phe
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,174,5551290
Polyers2,997,51684
Non-polymers177,0391206
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
2: 18S ribosomal RNA
S0: 40S ribosomal protein S0-A
S1: 40S ribosomal protein S1-A
S2: 40S ribosomal protein S2
S3: 40S ribosomal protein S3
S4: 40S ribosomal protein S4-A
S5: 40S ribosomal protein S5
S6: 40S ribosomal protein S6-A
S7: 40S ribosomal protein S7-A
S8: 40S ribosomal protein S8
S9: 40S ribosomal protein S9-A
C0: 40S ribosomal protein S10-A,40S Ribosomal Protein S10
C1: 40S ribosomal protein S11-A,40S Ribosomal Protein S11
C2: 40S Ribosomal Protein S12,40S ribosomal protein S12
C3: 40S ribosomal protein S13
C4: 40S ribosomal protein S14-A
C5: 40S Ribosomal Protein S15,40S ribosomal protein S15,40S Ribosomal Protein S15
C6: 40S ribosomal protein S16-A
C7: ES17
C8: 40S ribosomal protein S18-A
C9: 40S ribosomal protein S19-A
D0: 40S ribosomal protein S20
D1: 40S ribosomal protein S21-A
D2: 40S ribosomal protein S22-A
D3: 40S ribosomal protein S23-A
D4: 40S ribosomal protein S24-A
D5: 40S ribosomal protein S25-A
D6: 40S ribosomal protein S26-B
D7: 40S ribosomal protein S27-A
D8: 40S ribosomal protein S28-A
D9: 40S ribosomal protein S29-A
E0: 40S ribosomal protein S30-A
E1: Ubiquitin-40S ribosomal protein S31
SR: Guanine nucleotide-binding protein subunit beta-like protein
SM: Ribosome-bound protein Stm1,Suppressor protein STM1,Ribosome-bound protein Stm1
1: 25S ribosomal RNA
3: 5S ribosomal RNA
4: 5.8S ribosomal RNA
L2: 60S ribosomal protein L2-A
L3: 60S ribosomal protein L3
L4: 60S ribosomal protein L4-A
L5: 60S ribosomal protein L5
L6: 60S ribosomal protein L6-A
L7: 60S ribosomal protein L7-A
L8: 60S ribosomal protein L8-A
L9: 60S ribosomal protein L9-A
M0: 60S ribosomal protein L10
M1: 60S ribosomal protein L11-B
M3: 60S ribosomal protein L13-A
M4: 60S ribosomal protein L14-A
M5: 60S ribosomal protein L15-A
M6: 60S ribosomal protein L16-A
M7: 60S ribosomal protein L17-A
M8: 60S ribosomal protein L18-A
M9: 60S ribosomal protein L19-A
N0: 60S ribosomal protein L20-A
N1: 60S ribosomal protein L21-A
N2: 60S ribosomal protein L22-A
N3: 60S ribosomal protein L23-A
N4: 60S ribosomal protein L24-A
N5: 60S ribosomal protein L25
N6: 60S ribosomal protein L26-A
N7: 60S ribosomal protein L27-A
N8: 60S ribosomal protein L28
N9: 60S ribosomal protein L29
O0: 60S ribosomal protein L30
O1: 60S ribosomal protein L31-A
O2: 60S ribosomal protein L32
O3: 60S ribosomal protein L33-A
O4: 60S ribosomal protein L34-A
O5: 60S ribosomal protein L35-A
O6: 60S ribosomal protein L36-A
O7: 60S ribosomal protein L37-A
O8: 60S ribosomal protein L38
O9: 60S ribosomal protein L39
Q0: Ubiquitin-60S ribosomal protein L40
Q1: 60S ribosomal protein L41-A
Q2: 60S ribosomal protein L42-A
Q3: 60S ribosomal protein L43-A
P: Peptidyl-tRNA analog ACCA-Leu-Phe
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,135,4621184
Polyers2,966,93080
Non-polymers168,5331104
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)434.730, 286.770, 303.150
Angle α, β, γ (deg.)90.000, 98.870, 90.000
Int Tables number4
Space group name H-MP 1 21 1

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Components

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18S ribosomal ... , 2 types, 2 molecules 26

#1: RNA chain 18S ribosomal RNA /


Mass: 583803.688 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: GenBank: 768837785
#80: RNA chain 18S ribosomal RNA /


Mass: 579761.938 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: GenBank: 768837330

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40S Ribosomal Protein ... , 31 types, 60 molecules S0s0S1s1S2s2S3s3S4s4S5s5S6s6S7s7S8s8S9s9C0C1c1C2c2C3c3C4c4C5...

#2: Protein/peptide 40S ribosomal protein S0-A / Ribosome / Nucleic acid-binding protein NAB1A


Mass: 22811.074 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: B3LI22
#3: Protein/peptide 40S ribosomal protein S1-A / Ribosome


Mass: 24498.365 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: B3RHV0
#4: Protein/peptide 40S ribosomal protein S2 / / Omnipotent suppressor protein SUP44 / RP12 / S4 / YS5


Mass: 23212.979 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P25443
#5: Protein/peptide 40S ribosomal protein S3 / / RP13 / YS3


Mass: 24702.791 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05750
#6: Protein/peptide 40S ribosomal protein S4-A / Ribosome / RP5 / S7 / YS6


Mass: 29338.133 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX35
#7: Protein/peptide 40S ribosomal protein S5 / / RP14 / S2 / YS8


Mass: 22908.338 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P26783
#8: Protein/peptide 40S ribosomal protein S6-A / Ribosome / RP9 / S10 / YS4


Mass: 25895.072 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX37
#9: Protein/peptide 40S ribosomal protein S7-A / Ribosome / RP30 / RP40


Mass: 21158.648 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P26786
#10: Protein/peptide 40S ribosomal protein S8 /


Mass: 21147.180 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: A0A0J9X221
#11: Protein/peptide 40S ribosomal protein S9-A / Ribosome / RP21 / S13 / YP28 / YS11


Mass: 21210.662 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: O13516
#12: Protein/peptide 40S ribosomal protein S10-A,40S Ribosomal Protein S10 / Ribosome


Mass: 11137.772 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q08745
#13: Protein/peptide 40S ribosomal protein S11-A,40S Ribosomal Protein S11 / Ribosome / RP41 / S18 / YS12


Mass: 17368.424 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX47
#14: Protein/peptide 40S Ribosomal Protein S12,40S ribosomal protein S12 / Ribosome


Mass: 13239.271 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P48589
#15: Protein/peptide 40S ribosomal protein S13 / / S27a / YS15


Mass: 16928.748 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05756
#16: Protein/peptide 40S ribosomal protein S14-A / Ribosome / RP59A


Mass: 13560.528 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P06367
#17: Protein/peptide 40S Ribosomal Protein S15,40S ribosomal protein S15,40S Ribosomal Protein S15 / Ribosome / RIG protein / RP52 / S21 / YS21


Mass: 14977.639 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q01855
#18: Protein/peptide 40S ribosomal protein S16-A / Ribosome / RP61R


Mass: 15746.292 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX51
#20: Protein/peptide 40S ribosomal protein S18-A / Ribosome


Mass: 16940.443 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX55
#21: Protein/peptide 40S ribosomal protein S19-A / Ribosome / RP55A / S16a / YP45 / YS16A


Mass: 15810.930 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P07280
#22: Protein/peptide 40S ribosomal protein S20 /


Mass: 12575.547 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P38701
#23: Protein/peptide 40S ribosomal protein S21-A / Ribosome / S26 / YS25


Mass: 9758.829 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0C0V8
#24: Protein/peptide 40S ribosomal protein S22-A / Ribosome / RP50 / S24 / YP58 / YS22


Mass: 14518.867 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0C0W1
#25: Protein/peptide 40S ribosomal protein S23-A / Ribosome


Mass: 15942.699 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CY39
#26: Protein/peptide 40S ribosomal protein S24-A / Ribosome / RP50


Mass: 15231.650 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX31
#27: Protein/peptide 40S ribosomal protein S25-A / Ribosome / RP45 / S31 / YS23


Mass: 8001.377 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q3E792
#28: Protein/peptide 40S ribosomal protein S26-B / Ribosome


Mass: 11022.989 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P39939
#29: Protein/peptide 40S ribosomal protein S27-A / Ribosome / RP61 / YS20


Mass: 8762.195 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P35997
#30: Protein/peptide 40S ribosomal protein S28-A / Ribosome / S33 / YS27


Mass: 7116.281 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q3E7X9
#31: Protein/peptide 40S ribosomal protein S29-A / Ribosome / S36 / YS29


Mass: 6335.303 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P41057
#32: Protein/peptide 40S ribosomal protein S30-A / Ribosome


Mass: 7006.346 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX33
#81: Protein/peptide 40S ribosomal protein S10-A,40S Ribosomal Protein S10 / Ribosome


Mass: 11040.659 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q08745

+
Protein/peptide , 6 types, 8 molecules C7E1e1SMQ0q0c7sM

#19: Protein/peptide ES17


Mass: 13768.985 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: A0A0J9X224
#33: Protein/peptide Ubiquitin-40S ribosomal protein S31


Mass: 8703.462 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05759
#35: Protein/peptide Ribosome-bound protein Stm1,Suppressor protein STM1,Ribosome-bound protein Stm1 / 3BP1 / GU4 nucleic-binding protein 2 / G4p2 protein / POP2 multicopy suppressor protein 4 / Ribosomal subunits association factor / AF / TOM1 suppressor protein 1 / Triplex-binding protein 1


Mass: 16314.319 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P39015
#76: Protein/peptide Ubiquitin-60S ribosomal protein L40


Mass: 6032.321 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CH08
#82: Protein/peptide ES17


Mass: 13840.062 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: A0A0J9X224
#84: Protein/peptide Suppressor protein STM1,Ribosome-bound protein Stm1 / Silencer (firearms) / 3BP1 / GU4 nucleic-binding protein 2 / G4p2 protein / POP2 multicopy suppressor protein 4 / Ribosomal subunits association factor / AF / TOM1 suppressor protein 1 / Triplex-binding protein 1


Mass: 10310.914 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P39015

+
Guanine nucleotide-binding protein subunit beta-like ... , 2 types, 2 molecules SRsR

#34: Protein/peptide Guanine nucleotide-binding protein subunit beta-like protein / Receptor for activated C kinase / Receptor of activated protein kinase C 1 / RACK1


Mass: 34651.922 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P38011
#83: Protein/peptide Guanine nucleotide-binding protein subunit beta-like protein / Receptor for activated C kinase / Receptor of activated protein kinase C 1 / RACK1


Mass: 34710.023 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P38011

+
25S ribosomal ... , 2 types, 2 molecules 15

#36: RNA chain 25S ribosomal RNA /


Mass: 1017859.125 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: GenBank: 768840912
#85: RNA chain 25S ribosomal RNA /


Mass: 1018196.375 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: GenBank: 768840912

+
RNA chain , 3 types, 6 molecules 3748Pp

#37: RNA chain 5S ribosomal RNA /


Mass: 38951.105 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: GenBank: 1039024045
#38: RNA chain 5.8S ribosomal RNA /


Mass: 50682.922 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: GenBank: 1059791452
#91: RNA chain Peptidyl-tRNA analog ACCA-Leu-Phe


Mass: 740.591 Da / Num. of mol.: 2 / Source: (synth.) Homo sapiens (human)

+
60S Ribosomal Protein ... , 45 types, 84 molecules L2l2L3l3L4l4L5l5L6l6L7l7L8L9l9M0m0M1m1M3m3M4m4M5m5M6m6M7m7M8...

#39: Protein/peptide 60S ribosomal protein L2-A / Ribosome / L5 / RP8 / YL6


Mass: 27217.289 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX45
#40: Protein/peptide 60S ribosomal protein L3 / / Maintenance of killer protein 8 / RP1 / Trichodermin resistance protein / YL1


Mass: 43719.602 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P14126
#41: Protein/peptide 60S ribosomal protein L4-A / Ribosome / L2 / RP2 / YL2


Mass: 39027.926 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P10664
#42: Protein/peptide 60S ribosomal protein L5 / / L1 / L1a / Ribosomal 5S RNA-binding protein / YL3


Mass: 33633.633 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P26321
#43: Protein/peptide 60S ribosomal protein L6-A / Ribosome / L17 / RP18 / YL16


Mass: 19869.369 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q02326
#44: Protein/peptide 60S ribosomal protein L7-A / Ribosome / L6 / RP11 / YL8


Mass: 25341.480 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05737
#45: Protein/peptide 60S ribosomal protein L8-A / Ribosome / L4 / L4-2 / L7a-1 / Maintenance of killer protein 7 / RP6 / YL5


Mass: 25814.998 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P17076
#46: Protein/peptide 60S ribosomal protein L9-A / Ribosome / L8 / RP24 / YL11


Mass: 21605.061 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05738
#47: Protein/peptide 60S ribosomal protein L10 / / L9 / Ubiquinol-cytochrome C reductase complex subunit VI-requiring protein


Mass: 25279.271 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P41805
#48: Protein/peptide 60S ribosomal protein L11-B / Ribosome / L16 / RP39 / YL22


Mass: 19266.082 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q3E757
#49: Protein/peptide 60S ribosomal protein L13-A / Ribosome


Mass: 21956.312 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q12690
#50: Protein/peptide 60S ribosomal protein L14-A / Ribosome


Mass: 15063.870 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P36105
#51: Protein/peptide 60S ribosomal protein L15-A / Ribosome / L13 / RP15R / YL10 / YP18


Mass: 24351.162 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05748
#52: Protein/peptide 60S ribosomal protein L16-A / Ribosome / L13a / L21 / RP22 / YL15


Mass: 22028.951 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P26784
#53: Protein/peptide 60S ribosomal protein L17-A / Ribosome / L20A / YL17


Mass: 20458.322 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05740
#54: Protein/peptide 60S ribosomal protein L18-A / Ribosome / RP28


Mass: 20478.059 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX49
#55: Protein/peptide 60S ribosomal protein L19-A / Ribosome / L23 / RP15L / RP33 / YL14


Mass: 21631.121 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX82
#56: Protein/peptide 60S ribosomal protein L20-A / Ribosome / L18a


Mass: 20478.852 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX23
#57: Protein/peptide 60S ribosomal protein L21-A / Ribosome


Mass: 18148.066 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q02753
#58: Protein/peptide 60S ribosomal protein L22-A / Ribosome / L1c / RP4 / YL31


Mass: 11263.863 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05749
#59: Protein/peptide 60S ribosomal protein L23-A / Ribosome / L17a / YL32


Mass: 14362.755 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX41
#60: Protein/peptide 60S ribosomal protein L24-A / Ribosome / L30 / RP29 / YL21


Mass: 11369.424 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P04449
#61: Protein/peptide 60S ribosomal protein L25 / / RP16L / YL25 / YP42'


Mass: 13771.176 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P04456
#62: Protein/peptide 60S ribosomal protein L26-A / Ribosome / L33 / YL33


Mass: 14134.588 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05743
#63: Protein/peptide 60S ribosomal protein L27-A / Ribosome


Mass: 15437.166 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0C2H6
#64: Protein/peptide 60S ribosomal protein L28 / / L27a / L29 / RP44 / RP62 / YL24


Mass: 16630.471 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P02406
#65: Protein/peptide 60S ribosomal protein L29 / / YL43


Mass: 6560.688 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05747
#66: Protein/peptide 60S ribosomal protein L30 / / L32 / RP73 / YL38


Mass: 10902.664 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P14120
#67: Protein/peptide 60S ribosomal protein L31-A / Ribosome / L34 / YL28


Mass: 12649.754 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0C2H8
#68: Protein/peptide 60S ribosomal protein L32 /


Mass: 14478.054 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P38061
#69: Protein/peptide 60S ribosomal protein L33-A / Ribosome / L37 / RP47 / YL37


Mass: 12045.935 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05744
#70: Protein/peptide 60S ribosomal protein L34-A / Ribosome


Mass: 12608.831 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P87262
#71: Protein/peptide 60S ribosomal protein L35-A / Ribosome


Mass: 13811.444 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX84
#72: Protein/peptide 60S ribosomal protein L36-A / Ribosome / L39 / YL39


Mass: 11020.063 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05745
#73: Protein/peptide 60S ribosomal protein L37-A / Ribosome / L43 / YL35 / YP55


Mass: 9746.199 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P49166
#74: Protein/peptide 60S ribosomal protein L38 /


Mass: 8714.363 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P49167
#75: Protein/peptide 60S ribosomal protein L39 / / L46 / YL40


Mass: 6227.444 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P04650
#77: Protein/peptide 60S ribosomal protein L41-A / Ribosome / L47 / YL41


Mass: 3354.243 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX86
#78: Protein/peptide 60S ribosomal protein L42-A / Ribosome / L41 / YL27 / YP44


Mass: 12115.462 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX27
#79: Protein/peptide 60S ribosomal protein L43-A / Ribosome / L37a / YL35


Mass: 9981.756 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX25
#86: Protein/peptide 60S ribosomal protein L8-A,60S Ribosomal Protein L8 / Ribosome / L4 / L4-2 / L7a-1 / Maintenance of killer protein 7 / RP6 / YL5


Mass: 25493.742 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P17076
#87: Protein/peptide 60S Ribosomal Protein L12 /


Mass: 12783.750 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast)
#88: Protein/peptide 60S ribosomal protein L24-A / Ribosome / L30 / RP29 / YL21


Mass: 15506.229 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P04449
#89: Protein/peptide 60S Ribosomal Protein P0 /


Mass: 15627.240 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast)
#90: Protein/peptide 60S Ribosomal Protein P1/2 / Ribosome


Mass: 4017.944 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast)

+
Non-polymers , 7 types, 2310 molecules

#92: Chemical...
ChemComp-OHX / osmium (III) hexammine / osmium(6+) hexaazanide


Mass: 286.365 Da / Num. of mol.: 1095 / Formula: H12N6Os
#93: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1191 / Formula: Mg / Magnesium
#94: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Formula: Zn / Zinc
#95: Chemical ChemComp-PHE / PHENYLALANINE


Mass: 165.189 Da / Num. of mol.: 2 / Formula: C9H11NO2 / Phenylalanine
#96: Chemical ChemComp-LEU / LEUCINE


Mass: 131.173 Da / Num. of mol.: 2 / Formula: C6H13NO2 / Leucine
#97: Chemical ChemComp-SPS / SPARSOMYCIN


Mass: 361.437 Da / Num. of mol.: 2 / Formula: C13H19N3O5S2 / Sparsomycin
#98: Chemical ChemComp-8AN / 3'-amino-3'-deoxyadenosine 5'-(dihydrogen phosphate)


Mass: 346.236 Da / Num. of mol.: 2 / Formula: C10H15N6O6P

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.14 / Density percent sol: 60.83 %
Crystal growTemp: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG20000

-
Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Type: SOLEIL BEAMLINE PROXIMA 1 / Synchrotron site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Collection date: Oct 10, 2012
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 83.58 Å2 / D resolution high: 3.5 Å / D resolution low: 200 Å / Number obs: 918642 / Observed criterion sigma I: -3 / CC half: 0.988 / Rmerge I obs: 0.614 / NetI over sigmaI: 4.94 / Redundancy: 5 % / Percent possible obs: 99.8
Reflection shell

Diffraction ID: 1

Rmerge I obsHighest resolutionLowest resolutionMeanI over sigI obsCC halfPercent possible all
1.4433.5003.6001.0000.36399.600
1.1943.6003.7001.2000.44199.700
0.9483.7003.8001.4900.53899.700
0.7853.8003.9001.8500.63899.700
0.6753.9004.0002.1200.70999.700
0.3854.0005.0003.6700.87799.800
0.2035.0006.0006.3600.95999.900
1.6676.0007.0007.6200.896100.000
1.1297.0008.00010.1000.937100.000
0.8418.0009.00011.8100.948100.000
0.6279.00010.00014.2000.970100.000
0.33310.00025.00018.1400.989100.000
0.06625.00050.00031.9200.99899.900
0.05050.00075.00031.8700.99999.600
0.03675.000100.00021.6500.99777.400
0.358100.000150.0002.8700.99782.400
150.000

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software

Type: package

NameVersionClassificationContact authorLocationContact author emailLanguageDate
XSCALEdata scalingWolfgang Kabschhttp://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xscale_program.html
PHENIX1.10.1_2155refinementPaul D. Adamshttp://www.phenix-online.org/PDAdams[at]lbl.govC++
PDB_EXTRACT3.20data extractionPDBhttp://sw-tools.pdb.org/apps/PDB_EXTRACT/deposit[at]deposit.rcsb.orgC++June. 20, 2015
PHENIX1.10.1_2155phasingPaul D. Adamshttp://www.phenix-online.org/PDAdams[at]lbl.govC++
XDSdata reductionWolfgang Kabschhttp://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_program.html
RefineMethod to determine structure: MOLECULAR REPLACEMENT / Overall SU ML: 0.58 / Cross valid method: FREE R-VALUE / Sigma F: 0 / Overall phase error: 31.91
Solvent computationSolvent shrinkage radii: 0.8 Å / Solvent vdw probe radii: 1.2 Å
Displacement parametersB iso max: 181.56 Å2 / B iso mean: 64.7214 Å2 / B iso min: 24.57 Å2
Least-squares processR factor R free: 0.3119 / R factor R work: 0.2608 / R factor obs: 0.2619 / Highest resolution: 3.5 Å / Lowest resolution: 148.723 Å / Number reflection R free: 18368 / Number reflection obs: 918426 / Percent reflection R free: 2 / Percent reflection obs: 99.79
Refine hist #finalHighest resolution: 3.5 Å / Lowest resolution: 148.723 Å / B iso mean ligand: 66.2 / Number residues total: 33347
Number of atoms included #finalProtein: 179692 / Nucleic acid: 222858 / Ligand: 8918 / Solvent: 0 / Total: 411468
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.024439292
X-RAY DIFFRACTIONf_angle_d2.743651131
X-RAY DIFFRACTIONf_chiral_restr0.09879620
X-RAY DIFFRACTIONf_plane_restr0.01141827
X-RAY DIFFRACTIONf_dihedral_angle_d18.952237980
Refine LS shell

Refine ID: X-RAY DIFFRACTION / Total number of bins used: 30

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workNumber reflection allPercent reflection obs
3.50000.34910.30863.53986092982130430100.0000
3.53980.35560.30423.58146082981930427100.0000
3.58140.38640.31843.62516112993530546100.0000
3.62510.35440.29833.67106092983230441100.0000
3.67100.35950.29583.71936112992430535100.0000
3.71930.35830.29673.77036102988730497100.0000
3.77030.34400.28713.82416112994130552100.0000
3.82410.32400.27393.88126092989130500100.0000
3.88120.33380.26693.94196102987630486100.0000
3.94190.32680.26254.00656102989130501100.0000
4.00650.30930.25954.07566112994330554100.0000
4.07560.32470.25944.14976122992930541100.0000
4.14970.30440.25724.22956092987330482100.0000
4.22950.30740.25784.31596112994330554100.0000
4.31590.33100.26074.40976143004730661100.0000
4.40970.31190.26064.51236102990730517100.0000
4.51230.30940.25854.62526123003430646100.0000
4.62520.30550.25334.75026112995130562100.0000
4.75020.32220.26094.89006143007830692100.0000
4.89000.30850.25415.04796132997230585100.0000
5.04790.30670.24815.22836133004830661100.0000
5.22830.30290.24995.43766123002630638100.0000
5.43760.31610.25085.68516133002430637100.0000
5.68510.28550.24995.98486163015330769100.0000
5.98480.31050.25116.35986133008130694100.0000
6.35980.30630.25506.85096163016530781100.0000
6.85090.30750.24727.54036153014530760100.0000
7.54030.29020.24358.63136163016930785100.0000
8.63130.27780.242510.87406173031330930100.0000
10.87400.26420.2507148.8569622304403106299.0000

+
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