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- PDB-8cq7: Crystal structure of phyllanthoside bound to the Candida albicans... -

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Basic information

Entry
Database: PDB / ID: 8cq7
TitleCrystal structure of phyllanthoside bound to the Candida albicans 80S ribosome
Components
  • (40S ribosomal protein ...) x 25
  • (60S ribosomal protein ...) x 38
  • (Ribosomal protein ...) x 10
  • 18S
  • 25S
  • 5.8S
  • 5S
  • 60S acidic ribosomal protein P0
  • Guanine nucleotide-binding protein subunit beta-like protein
  • Ribosomal protein
  • Ubiquitin-40S ribosomal protein S31 fusion protein
  • Uncharacterized protein CaJ7.0206
KeywordsRIBOSOME / Candida albicans / phyllanthoside
Function / homology
Function and homology information


yeast-form cell wall / hyphal cell wall / triplex DNA binding / ribosome hibernation / translation elongation factor binding / regulation of translational initiation in response to stress / pre-mRNA 5'-splice site binding / telomeric DNA binding / negative regulation of mRNA splicing, via spliceosome / translational elongation ...yeast-form cell wall / hyphal cell wall / triplex DNA binding / ribosome hibernation / translation elongation factor binding / regulation of translational initiation in response to stress / pre-mRNA 5'-splice site binding / telomeric DNA binding / negative regulation of mRNA splicing, via spliceosome / translational elongation / TOR signaling / protein-RNA complex assembly / ribosomal subunit export from nucleus / translation regulator activity / translation repressor activity / maturation of LSU-rRNA / cytosolic ribosome / telomere maintenance / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / small-subunit processome / maintenance of translational fidelity / modification-dependent protein catabolic process / protein tag activity / rRNA processing / large ribosomal subunit / ribosome biogenesis / ribosome binding / ribosomal small subunit assembly / large ribosomal subunit rRNA binding / small ribosomal subunit / 5S rRNA binding / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome / protein ubiquitination / translation / ribonucleoprotein complex / ubiquitin protein ligase binding / negative regulation of apoptotic process / cell surface / RNA binding / zinc ion binding / extracellular region / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
RNA binding protein HABP4/SERBP1 / Stm1-like, N-terminal / Stm1 / Hyaluronan/mRNA-binding protein / Hyaluronan / mRNA binding family / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / : / 50S ribosomal protein L10, insertion domain superfamily / : ...RNA binding protein HABP4/SERBP1 / Stm1-like, N-terminal / Stm1 / Hyaluronan/mRNA-binding protein / Hyaluronan / mRNA binding family / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / : / 50S ribosomal protein L10, insertion domain superfamily / : / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S26e / Ribosomal protein S21e, conserved site / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S21e signature. / : / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein L1, conserved site / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein L1 signature. / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L1 / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein L22e / Ribosomal protein L22e superfamily / S27a-like superfamily / Ribosomal L22e protein family / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / 40S Ribosomal protein S10 / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L44e signature. / Plectin/S10, N-terminal / Ribosomal protein L10e, conserved site / Plectin/S10 domain / Ribosomal protein L10e signature. / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L10e / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L19, eukaryotic / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S30 / : / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / : / Ribosomal protein S7e signature. / Ribosomal protein L24e, conserved site / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L24e signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / : / Ribosomal protein L30e signature 1. / Ribosomal protein L6e signature. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein S19e / Ribosomal protein S3Ae, conserved site / Ribosomal protein S19e / Ribosomal protein S3Ae signature. / Ribosomal_S19e / Ribosomal protein S27e signature. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal L40e family / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature.
Similarity search - Domain/homology
Chem-3K5 / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS4 ...Chem-3K5 / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS4 / Large ribosomal subunit protein eL37 / Large ribosomal subunit protein eL38 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein eL19 / Ribosome-associated protein STM1 / Large ribosomal subunit protein eL40 / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein eL30 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein eL43 / Small ribosomal subunit protein eS30 / Small ribosomal subunit protein uS14 / 60S ribosomal protein L42-B / Ribosomal protein S7 / 40S ribosomal protein S17-B / 40S ribosomal protein S26 / Ribosomal protein L22 / 60S ribosomal protein L7-A / 60S ribosomal protein L28 / 60S ribosomal protein L33-A / 40S ribosomal protein S27 / 40S ribosomal protein S10-A / Ribosomal protein S10 / 40S ribosomal protein S3 / 40S ribosomal protein S6 / Ribosomal protein L13 / Ribosomal protein S5 / 60S ribosomal protein L20 / 40S ribosomal protein S28-B / 60S ribosomal protein L8 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein uS2 / 40S ribosomal protein S12 / Guanine nucleotide-binding protein subunit beta-like protein / 40S ribosomal protein S24 / 60S ribosomal protein L9-B / 60S ribosomal protein L23-A / 60S ribosomal protein L24-A / 60S ribosomal protein L18-A / 40S ribosomal protein S19-A / 60S ribosomal protein L12-A / 40S ribosomal protein S7 / 40S ribosomal protein S25 / 60S ribosomal protein L29 / 40S ribosomal protein S22-A / 40S ribosomal protein S8 / Ribosomal protein S23 (S12) / 40S ribosomal protein S14-A / 60S ribosomal protein L34-B / 60S ribosomal protein L21-A / 60S ribosomal protein L31-B / 60S ribosomal protein L11-B / Ribosomal protein S4 / 60S ribosomal protein L2-B / 60S ribosomal protein L14-B / Ribosomal protein L24 / 40S ribosomal protein S18-B / Ribosomal protein / 40S ribosomal protein S13 / 60S ribosomal protein L4-B / 60S ribosomal protein L13 / 60S ribosomal protein L25 / Ribosomal protein L29 / 60S acidic ribosomal protein P0 / Uncharacterized protein CaJ7.0206 / Large ribosomal subunit protein eL32 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein eL36 / Small ribosomal subunit protein eS32 / Large ribosomal subunit protein uL3 / Ubiquitin-ribosomal protein eS31 fusion protein / Large ribosomal subunit protein eL15 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein eL39 / 60S ribosomal protein L6 / Large ribosomal subunit protein eL27 / Small ribosomal subunit protein eS21
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsKolosova, O. / Zgadzay, Y. / Yusupov, M.
Funding support France, Russian Federation, 4items
OrganizationGrant numberCountry
Foundation for Medical Research (France)DEQ20181039600 France
Foundation for Medical Research (France)DBF20160635745 France
Foundation for Medical Research (France)FDT202204014886 France
Russian Science Foundation20-65-47031 Russian Federation
CitationJournal: To Be Published
Title: Drug-induced rotational movement of the ribosome is a key factor for read-through enhancement
Authors: Kolosova, O. / Zgadzay, Y. / Yusupov, M.
History
DepositionMar 3, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: 25S
3: 5S
4: 5.8S
j: 60S ribosomal protein L2-B
k: 60S ribosomal protein L3
l: 60S ribosomal protein L4-B
m: Uncharacterized protein CaJ7.0206
n: 60S ribosomal protein L6
o: 60S ribosomal protein L7-A
p: 60S ribosomal protein L8
q: 60S ribosomal protein L9-B
r: 60S ribosomal protein L10
s: 60S ribosomal protein L11-B
t: 60S ribosomal protein L13
u: 60S ribosomal protein L14-B
v: 60S ribosomal protein L15-A
w: Ribosomal protein L13
x: Ribosomal protein L22
y: 60S ribosomal protein L18-A
z: 60S ribosomal protein L19-A
0: 60S ribosomal protein L20
2: 60S ribosomal protein L21-A
5: 60S ribosomal protein L22-B
6: 60S ribosomal protein L23-A
7: 60S ribosomal protein L24-A
8: 60S ribosomal protein L25
9: Ribosomal protein L24
AA: 60S ribosomal protein L27
AB: 60S ribosomal protein L28
AC: 60S ribosomal protein L29
AD: 60S ribosomal protein L30
AE: 60S ribosomal protein L31-B
AF: 60S ribosomal protein L32
AG: 60S ribosomal protein L33-A
AH: 60S ribosomal protein L34-B
AI: Ribosomal protein L29
AJ: 60S ribosomal protein L36
AK: 60S ribosomal protein L37-B
AL: 60S ribosomal protein L38
AM: 60S ribosomal protein L39
AN: 60S ribosomal protein L40-B
AO: 60S ribosomal protein L41
AP: 60S ribosomal protein L42-B
AQ: 60S ribosomal protein L43-A
i: 60S ribosomal protein CAALFM_C304810CA
B: 18S
C: 40S ribosomal protein S0
D: 40S ribosomal protein S1
E: Ribosomal protein S5
F: Ribosomal protein S3
G: 40S ribosomal protein S4
H: Ribosomal protein S7
I: 40S ribosomal protein S6
J: 40S ribosomal protein S7
K: 40S ribosomal protein S8
L: Ribosomal protein S4
M: 40S ribosomal protein S10-A
N: 40S ribosomal protein S11A
P: 40S ribosomal protein S13
Q: 40S ribosomal protein S14-A
R: 40S ribosomal protein S15
S: 40S ribosomal protein S16
T: 40S ribosomal protein S17-B
U: 40S ribosomal protein S18-B
V: 40S ribosomal protein S19-A
W: Ribosomal protein S10
X: 40S ribosomal protein S21
Y: 40S ribosomal protein S22-A
Z: Ribosomal protein S23 (S12)
a: 40S ribosomal protein S24
b: 40S ribosomal protein S25
c: 40S ribosomal protein S26
d: 40S ribosomal protein S27
e: 40S ribosomal protein S28-B
f: 40S ribosomal protein S29A
g: 40S ribosomal protein S30
h: Ubiquitin-40S ribosomal protein S31 fusion protein
AR: Guanine nucleotide-binding protein subunit beta-like protein
AS: 25S
AT: 5S
AU: 5.8S
AW: 60S ribosomal protein L2-B
AX: 60S ribosomal protein L3
AY: 60S ribosomal protein L4-B
AZ: Uncharacterized protein CaJ7.0206
BA: 60S ribosomal protein L6
BB: 60S ribosomal protein L7-A
BC: 60S ribosomal protein L8
BD: 60S ribosomal protein L9-B
BE: 60S ribosomal protein L10
BF: 60S ribosomal protein L11-B
BG: 60S ribosomal protein L13
BH: 60S ribosomal protein L14-B
BI: 60S ribosomal protein L15-A
BJ: Ribosomal protein L13
BK: Ribosomal protein L22
BL: 60S ribosomal protein L18-A
BM: 60S ribosomal protein L19-A
BN: 60S ribosomal protein L20
BO: 60S ribosomal protein L21-A
BP: 60S ribosomal protein L22-B
BQ: 60S ribosomal protein L23-A
BR: 60S ribosomal protein L24-A
BS: 60S ribosomal protein L25
BT: Ribosomal protein L24
BU: 60S ribosomal protein L27
BV: 60S ribosomal protein L28
BW: 60S ribosomal protein L29
BX: 60S ribosomal protein L30
BY: 60S ribosomal protein L31-B
BZ: 60S ribosomal protein L32
CA: 60S ribosomal protein L33-A
CB: 60S ribosomal protein L34-B
CC: Ribosomal protein L29
CD: 60S ribosomal protein L36
CE: 60S ribosomal protein L37-B
CF: 60S ribosomal protein L38
CG: 60S ribosomal protein L39
CH: 60S ribosomal protein L40-B
CI: 60S ribosomal protein L41
CJ: 60S ribosomal protein L42-B
CK: 60S ribosomal protein L43-A
CL: 60S ribosomal protein CAALFM_C304810CA
CM: 18S
CN: 40S ribosomal protein S0
CO: 40S ribosomal protein S1
CP: Ribosomal protein S5
CQ: Ribosomal protein S3
CR: 40S ribosomal protein S4
CS: Ribosomal protein S7
CT: 40S ribosomal protein S6
CU: 40S ribosomal protein S7
CV: 40S ribosomal protein S8
CW: Ribosomal protein S4
CX: 40S ribosomal protein S10-A
CY: 40S ribosomal protein S11A
CZ: 40S ribosomal protein S12
DA: 40S ribosomal protein S13
DB: 40S ribosomal protein S14-A
DC: 40S ribosomal protein S15
DD: 40S ribosomal protein S16
DE: 40S ribosomal protein S17-B
DF: 40S ribosomal protein S18-B
DG: 40S ribosomal protein S19-A
DH: Ribosomal protein S10
DI: 40S ribosomal protein S21
DJ: 40S ribosomal protein S22-A
DK: Ribosomal protein S23 (S12)
DL: 40S ribosomal protein S24
DM: 40S ribosomal protein S25
DN: 40S ribosomal protein S26
DO: 40S ribosomal protein S27
DP: 40S ribosomal protein S28-B
DQ: 40S ribosomal protein S29A
DR: 40S ribosomal protein S30
DS: Ubiquitin-40S ribosomal protein S31 fusion protein
DT: Guanine nucleotide-binding protein subunit beta-like protein
P0: 60S acidic ribosomal protein P0
12: 60S ribosomal protein L12-A
L1: Ribosomal protein
l1: Ribosomal protein
p0: 60S acidic ribosomal protein P0
O: 40S ribosomal protein S12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,414,2351839
Polymers6,371,199163
Non-polymers43,0361676
Water1,08160
1
1: 25S
3: 5S
4: 5.8S
j: 60S ribosomal protein L2-B
k: 60S ribosomal protein L3
l: 60S ribosomal protein L4-B
m: Uncharacterized protein CaJ7.0206
n: 60S ribosomal protein L6
o: 60S ribosomal protein L7-A
p: 60S ribosomal protein L8
q: 60S ribosomal protein L9-B
r: 60S ribosomal protein L10
s: 60S ribosomal protein L11-B
t: 60S ribosomal protein L13
u: 60S ribosomal protein L14-B
v: 60S ribosomal protein L15-A
w: Ribosomal protein L13
x: Ribosomal protein L22
y: 60S ribosomal protein L18-A
z: 60S ribosomal protein L19-A
0: 60S ribosomal protein L20
2: 60S ribosomal protein L21-A
5: 60S ribosomal protein L22-B
6: 60S ribosomal protein L23-A
7: 60S ribosomal protein L24-A
8: 60S ribosomal protein L25
9: Ribosomal protein L24
AA: 60S ribosomal protein L27
AB: 60S ribosomal protein L28
AC: 60S ribosomal protein L29
AD: 60S ribosomal protein L30
AE: 60S ribosomal protein L31-B
AF: 60S ribosomal protein L32
AG: 60S ribosomal protein L33-A
AH: 60S ribosomal protein L34-B
AI: Ribosomal protein L29
AJ: 60S ribosomal protein L36
AK: 60S ribosomal protein L37-B
AL: 60S ribosomal protein L38
AM: 60S ribosomal protein L39
AN: 60S ribosomal protein L40-B
AO: 60S ribosomal protein L41
AP: 60S ribosomal protein L42-B
AQ: 60S ribosomal protein L43-A
i: 60S ribosomal protein CAALFM_C304810CA
B: 18S
C: 40S ribosomal protein S0
D: 40S ribosomal protein S1
E: Ribosomal protein S5
F: Ribosomal protein S3
G: 40S ribosomal protein S4
H: Ribosomal protein S7
I: 40S ribosomal protein S6
J: 40S ribosomal protein S7
K: 40S ribosomal protein S8
L: Ribosomal protein S4
M: 40S ribosomal protein S10-A
N: 40S ribosomal protein S11A
P: 40S ribosomal protein S13
Q: 40S ribosomal protein S14-A
R: 40S ribosomal protein S15
S: 40S ribosomal protein S16
T: 40S ribosomal protein S17-B
U: 40S ribosomal protein S18-B
V: 40S ribosomal protein S19-A
W: Ribosomal protein S10
X: 40S ribosomal protein S21
Y: 40S ribosomal protein S22-A
Z: Ribosomal protein S23 (S12)
a: 40S ribosomal protein S24
b: 40S ribosomal protein S25
c: 40S ribosomal protein S26
d: 40S ribosomal protein S27
e: 40S ribosomal protein S28-B
f: 40S ribosomal protein S29A
g: 40S ribosomal protein S30
h: Ubiquitin-40S ribosomal protein S31 fusion protein
AR: Guanine nucleotide-binding protein subunit beta-like protein
P0: 60S acidic ribosomal protein P0
12: 60S ribosomal protein L12-A
l1: Ribosomal protein
O: 40S ribosomal protein S12
hetero molecules


  • defined by author
  • 3.22 MDa, 82 polymers
Theoretical massNumber of molelcules
Total (without water)3,219,1731050
Polymers3,194,49582
Non-polymers24,678968
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
AS: 25S
AT: 5S
AU: 5.8S
AW: 60S ribosomal protein L2-B
AX: 60S ribosomal protein L3
AY: 60S ribosomal protein L4-B
AZ: Uncharacterized protein CaJ7.0206
BA: 60S ribosomal protein L6
BB: 60S ribosomal protein L7-A
BC: 60S ribosomal protein L8
BD: 60S ribosomal protein L9-B
BE: 60S ribosomal protein L10
BF: 60S ribosomal protein L11-B
BG: 60S ribosomal protein L13
BH: 60S ribosomal protein L14-B
BI: 60S ribosomal protein L15-A
BJ: Ribosomal protein L13
BK: Ribosomal protein L22
BL: 60S ribosomal protein L18-A
BM: 60S ribosomal protein L19-A
BN: 60S ribosomal protein L20
BO: 60S ribosomal protein L21-A
BP: 60S ribosomal protein L22-B
BQ: 60S ribosomal protein L23-A
BR: 60S ribosomal protein L24-A
BS: 60S ribosomal protein L25
BT: Ribosomal protein L24
BU: 60S ribosomal protein L27
BV: 60S ribosomal protein L28
BW: 60S ribosomal protein L29
BX: 60S ribosomal protein L30
BY: 60S ribosomal protein L31-B
BZ: 60S ribosomal protein L32
CA: 60S ribosomal protein L33-A
CB: 60S ribosomal protein L34-B
CC: Ribosomal protein L29
CD: 60S ribosomal protein L36
CE: 60S ribosomal protein L37-B
CF: 60S ribosomal protein L38
CG: 60S ribosomal protein L39
CH: 60S ribosomal protein L40-B
CI: 60S ribosomal protein L41
CJ: 60S ribosomal protein L42-B
CK: 60S ribosomal protein L43-A
CL: 60S ribosomal protein CAALFM_C304810CA
CM: 18S
CN: 40S ribosomal protein S0
CO: 40S ribosomal protein S1
CP: Ribosomal protein S5
CQ: Ribosomal protein S3
CR: 40S ribosomal protein S4
CS: Ribosomal protein S7
CT: 40S ribosomal protein S6
CU: 40S ribosomal protein S7
CV: 40S ribosomal protein S8
CW: Ribosomal protein S4
CX: 40S ribosomal protein S10-A
CY: 40S ribosomal protein S11A
CZ: 40S ribosomal protein S12
DA: 40S ribosomal protein S13
DB: 40S ribosomal protein S14-A
DC: 40S ribosomal protein S15
DD: 40S ribosomal protein S16
DE: 40S ribosomal protein S17-B
DF: 40S ribosomal protein S18-B
DG: 40S ribosomal protein S19-A
DH: Ribosomal protein S10
DI: 40S ribosomal protein S21
DJ: 40S ribosomal protein S22-A
DK: Ribosomal protein S23 (S12)
DL: 40S ribosomal protein S24
DM: 40S ribosomal protein S25
DN: 40S ribosomal protein S26
DO: 40S ribosomal protein S27
DP: 40S ribosomal protein S28-B
DQ: 40S ribosomal protein S29A
DR: 40S ribosomal protein S30
DS: Ubiquitin-40S ribosomal protein S31 fusion protein
DT: Guanine nucleotide-binding protein subunit beta-like protein
L1: Ribosomal protein
p0: 60S acidic ribosomal protein P0
hetero molecules


  • defined by author
  • 3.2 MDa, 81 polymers
Theoretical massNumber of molelcules
Total (without water)3,195,062789
Polymers3,176,70381
Non-polymers18,358708
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)299.770, 294.170, 451.170
Angle α, β, γ (deg.)90.00, 100.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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RNA chain , 4 types, 8 molecules 1AS3AT4AUBCM

#1: RNA chain 25S


Mass: 1085278.125 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: GenBank: XR_002086444.1
#2: RNA chain 5S


Mass: 38943.129 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: GenBank: X16634.1
#3: RNA chain 5.8S


Mass: 50683.906 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: GenBank: OQ195134.1
#46: RNA chain 18S


Mass: 575838.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: GenBank: XR_002086442.1

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60S ribosomal protein ... , 38 types, 75 molecules jAWkAXlAYnBAoBBpBCqBDrBEsBFtBGuBHvBIyBLzBM0BN...

#4: Protein 60S ribosomal protein L2-B


Mass: 27366.596 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F1X9
#5: Protein 60S ribosomal protein L3


Mass: 44040.848 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: Q59LS1
#6: Protein 60S ribosomal protein L4-B


Mass: 39282.352 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F4H4
#8: Protein 60S ribosomal protein L6


Mass: 19798.002 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: Q9P834
#9: Protein 60S ribosomal protein L7-A


Mass: 27446.961 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BVN2
#10: Protein 60S ribosomal protein L8


Mass: 28549.424 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C337
#11: Protein 60S ribosomal protein L9-B


Mass: 21755.217 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C3N3
#12: Protein 60S ribosomal protein L10


Mass: 25236.297 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: Q5AIB8
#13: Protein 60S ribosomal protein L11-B


Mass: 19859.805 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F1S5
#14: Protein 60S ribosomal protein L13


Mass: 23105.771 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F5V7
#15: Protein 60S ribosomal protein L14-B


Mass: 14748.476 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F332
#16: Protein 60S ribosomal protein L15-A


Mass: 24389.256 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: Q5A6R1
#19: Protein 60S ribosomal protein L18-A


Mass: 20817.367 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C4Y1
#20: Protein 60S ribosomal protein L19-A


Mass: 21942.750 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A1D8PK40
#21: Protein 60S ribosomal protein L20


Mass: 20376.859 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BZJ3
#22: Protein 60S ribosomal protein L21-A


Mass: 18049.945 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F1C8
#23: Protein 60S ribosomal protein L22-B


Mass: 14107.862 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A1D8PM41
#24: Protein 60S ribosomal protein L23-A


Mass: 14494.999 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C444
#25: Protein 60S ribosomal protein L24-A


Mass: 17430.322 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C4U1
#26: Protein 60S ribosomal protein L25


Mass: 15873.581 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F6A1
#28: Protein 60S ribosomal protein L27


Mass: 15551.407 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: Q9P843
#29: Protein 60S ribosomal protein L28


Mass: 16703.367 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BVY8
#30: Protein 60S ribosomal protein L29


Mass: 7135.336 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F0G8
#31: Protein 60S ribosomal protein L30


Mass: 11520.384 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A1D8PM75
#32: Protein 60S ribosomal protein L31-B


Mass: 12993.149 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F1M1
#33: Protein 60S ribosomal protein L32


Mass: 14993.688 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: O94008
#34: Protein 60S ribosomal protein L33-A


Mass: 12138.237 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BW57
#35: Protein 60S ribosomal protein L34-B


Mass: 13774.282 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F171
#37: Protein 60S ribosomal protein L36 / L39


Mass: 11096.161 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: P47834
#38: Protein 60S ribosomal protein L37-B


Mass: 10102.830 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A1D8PF45
#39: Protein 60S ribosomal protein L38


Mass: 8911.532 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A1D8PG16
#40: Protein 60S ribosomal protein L39 / L46


Mass: 6347.549 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: Q96W55
#41: Protein 60S ribosomal protein L40-B


Mass: 6078.412 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A1D8PL68
#42: Protein/peptide 60S ribosomal protein L41


Mass: 3396.280 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: P9WER7
#43: Protein 60S ribosomal protein L42-B


Mass: 12259.631 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BR69
#44: Protein 60S ribosomal protein L43-A


Mass: 10136.844 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A1D8PP14
#45: Protein 60S ribosomal protein CAALFM_C304810CA


Mass: 29126.141 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A1D8PK71
#81: Protein 60S ribosomal protein L12-A


Mass: 17791.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C5X8

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Protein , 5 types, 10 molecules mAZhDSARDTP0p0L1l1

#7: Protein Uncharacterized protein CaJ7.0206


Mass: 34557.977 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: G1UAA6
#77: Protein Ubiquitin-40S ribosomal protein S31 fusion protein


Mass: 22615.525 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: Q5A109
#78: Protein Guanine nucleotide-binding protein subunit beta-like protein


Mass: 34593.934 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C3E7
#80: Protein 60S acidic ribosomal protein P0


Mass: 33302.633 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: G1UA71
#82: Protein Ribosomal protein


Mass: 24416.736 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F4E7

-
Ribosomal protein ... , 10 types, 20 molecules wBJxBK9BTAICCECPFCQHCSLCWWDHZDK

#17: Protein Ribosomal protein L13


Mass: 22685.850 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BZ56
#18: Protein Ribosomal protein L22


Mass: 21002.861 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BUG0
#27: Protein Ribosomal protein L24


Mass: 14215.550 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F3X2
#36: Protein Ribosomal protein L29


Mass: 14118.759 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F6B7
#49: Protein Ribosomal protein S5


Mass: 26917.314 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BZ90
#50: Protein Ribosomal protein S3


Mass: 27313.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BYS1
#52: Protein Ribosomal protein S7


Mass: 25319.922 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BS29
#56: Protein Ribosomal protein S4


Mass: 21765.146 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F1X2
#66: Protein Ribosomal protein S10


Mass: 13366.540 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BYJ9
#69: Protein Ribosomal protein S23 (S12)


Mass: 16000.784 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F0V0

+
40S ribosomal protein ... , 25 types, 50 molecules CCNDCOGCRICTJCUKCVMCXNCYPDAQDBRDCSDDTDEUDFVDG...

#47: Protein 40S ribosomal protein S0


Mass: 28759.307 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C395
#48: Protein 40S ribosomal protein S1


Mass: 29041.859 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C387
#51: Protein 40S ribosomal protein S4


Mass: 29435.354 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A1D8PCI6
#53: Protein 40S ribosomal protein S6


Mass: 27146.469 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BZ37
#54: Protein 40S ribosomal protein S7


Mass: 21285.818 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C655
#55: Protein 40S ribosomal protein S8


Mass: 22801.979 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F0S0
#57: Protein 40S ribosomal protein S10-A


Mass: 13836.824 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BWQ8
#58: Protein 40S ribosomal protein S11A


Mass: 17638.648 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A1D8PN83
#59: Protein 40S ribosomal protein S13


Mass: 16976.787 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F4G0
#60: Protein 40S ribosomal protein S14-A


Mass: 14052.112 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F0V4
#61: Protein 40S ribosomal protein S15


Mass: 15967.796 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A1D8PK22
#62: Protein 40S ribosomal protein S16


Mass: 15769.456 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: O94017
#63: Protein 40S ribosomal protein S17-B


Mass: 15770.298 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BTR7
#64: Protein 40S ribosomal protein S18-B


Mass: 17023.785 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F3Y8
#65: Protein 40S ribosomal protein S19-A


Mass: 16097.218 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C5L4
#67: Protein 40S ribosomal protein S21


Mass: 9652.814 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: Q9P844
#68: Protein 40S ribosomal protein S22-A


Mass: 14807.189 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F0N4
#70: Protein 40S ribosomal protein S24


Mass: 15546.922 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C3K1
#71: Protein 40S ribosomal protein S25


Mass: 11633.762 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6EZQ8
#72: Protein 40S ribosomal protein S26


Mass: 13606.099 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BTS1
#73: Protein 40S ribosomal protein S27


Mass: 8982.504 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BWE6
#74: Protein 40S ribosomal protein S28-B


Mass: 7536.808 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C0A5
#75: Protein 40S ribosomal protein S29A


Mass: 6615.582 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A1D8PTR4
#76: Protein 40S ribosomal protein S30


Mass: 7127.437 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A1D8PSK2
#79: Protein 40S ribosomal protein S12


Mass: 15715.855 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C3A1

-
Non-polymers , 4 types, 1736 molecules

#83: Chemical ChemComp-3K5 / 3-O-acetyl-2-O-(3-O-acetyl-6-deoxy-beta-D-glucopyranosyl)-6-deoxy-1-O-{[(2R,2'S,3a'R,4''S,5''R,6'S,7a'S)-5''-methyl-4''-{[(2E)-3-phenylprop-2-enoyl]oxy}decahydrodispiro[oxirane-2,3'-[1]benzofuran-2',2''-pyran]-6'-yl]carbonyl}-beta-D-glucopyranose / Phyllanthoside


Mass: 804.831 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H52O17
#84: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1656 / Source method: obtained synthetically / Formula: Mg
#85: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Zn
#86: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.28 Å3/Da / Density % sol: 62.5 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 20K, KSCN, Mg Acetate, K - acetate, Bis-Tris-Acetate, Glycerol, Spermidine, phyllanthoside

-
Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→228.18 Å / Num. obs: 1261990 / % possible obs: 100 % / Redundancy: 21.5 % / Biso Wilson estimate: 79.31 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.736 / Rrim(I) all: 0.753 / Net I/σ(I): 4.7
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
3.2-3.253.471571410.0693.5521
3.25-3.33.378538460.093.4561
3.3-3.353.232505450.1013.3081
3.35-3.43.123476740.1343.1961
3.4-3.453.024451200.1493.0961
3.45-3.52.831424500.1882.8981
3.5-3.552.705400450.2122.7691
3.55-3.62.567378560.2632.6291
3.6-3.72.341698960.3152.3991
3.7-3.82.035626500.4172.0861
3.8-3.91.782564270.4941.8321
3.9-41.624509430.6021.6631
4-4.51.2171920850.7991.2461
4.5-70.5573336790.9610.571
7-100.217796810.9940.2221
10-500.083416560.9990.0851
50-228.180.0932960.9960.0961

-
Processing

Software
NameVersionClassification
PHENIX1.19rc4_4035refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→228.18 Å / SU ML: 0.64 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2811 2000 0.16 %
Rwork0.2465 --
obs0.2466 1261843 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→228.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms182490 224518 1848 0 408856
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003438368
X-RAY DIFFRACTIONf_angle_d0.792643002
X-RAY DIFFRACTIONf_dihedral_angle_d16.089151941
X-RAY DIFFRACTIONf_chiral_restr0.04480486
X-RAY DIFFRACTIONf_plane_restr0.00642481
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.280.39861420.378189691X-RAY DIFFRACTION100
3.28-3.370.41681430.376689883X-RAY DIFFRACTION100
3.37-3.470.39881430.363489718X-RAY DIFFRACTION100
3.47-3.580.36071420.342489829X-RAY DIFFRACTION100
3.58-3.710.33361430.319589782X-RAY DIFFRACTION100
3.71-3.860.31251420.295189916X-RAY DIFFRACTION100
3.86-4.030.32391430.275289869X-RAY DIFFRACTION100
4.03-4.240.2791430.250589888X-RAY DIFFRACTION100
4.24-4.510.29381420.229789937X-RAY DIFFRACTION100
4.51-4.860.25751430.211989954X-RAY DIFFRACTION100
4.86-5.350.25141430.199190147X-RAY DIFFRACTION100
5.35-6.120.24081430.194990141X-RAY DIFFRACTION100
6.12-7.710.25171430.201990259X-RAY DIFFRACTION100
7.71-228.180.20571450.193790829X-RAY DIFFRACTION100

+
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