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- PDB-7m57: Crystallographic structure of a primitive orthorhombic crystal fo... -

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Basic information

Entry
Database: PDB / ID: 7m57
TitleCrystallographic structure of a primitive orthorhombic crystal form of STMV
Components
  • Coat protein
  • RNA (27-mer)
  • RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
KeywordsVIRUS/RNA / VIRUS-RNA complex
Function / homologySatellite virus coat domain superfamily / viral capsid / structural molecule activity / PHOSPHATE ION / RNA / RNA (> 10) / Coat protein
Function and homology information
Biological speciesSatellite tobacco mosaic virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsMcPherson, A.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2021
Title: Structures of additional crystal forms of Satellite tobacco mosaic virus grown from a variety of salts.
Authors: McPherson, A.
History
DepositionMar 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Coat protein
B: Coat protein
C: Coat protein
D: Coat protein
E: Coat protein
F: Coat protein
G: Coat protein
H: Coat protein
I: Coat protein
J: Coat protein
K: Coat protein
L: Coat protein
M: Coat protein
N: Coat protein
O: Coat protein
P: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
Q: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
R: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
S: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
T: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
U: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
V: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
W: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
X: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
Y: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
Z: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
a: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
b: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
c: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
d: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
e: RNA (27-mer)
f: RNA (27-mer)
g: RNA (27-mer)
h: RNA (27-mer)
i: RNA (27-mer)
j: RNA (27-mer)
k: RNA (27-mer)
l: RNA (27-mer)
m: RNA (27-mer)
n: RNA (27-mer)
o: RNA (27-mer)
p: RNA (27-mer)
q: RNA (27-mer)
r: RNA (27-mer)
s: RNA (27-mer)
t: RNA (27-mer)
u: RNA (27-mer)
v: RNA (27-mer)
w: RNA (27-mer)
x: RNA (27-mer)
y: RNA (27-mer)
z: RNA (27-mer)
1: RNA (27-mer)
2: RNA (27-mer)
3: RNA (27-mer)
4: RNA (27-mer)
5: RNA (27-mer)
6: RNA (27-mer)
7: RNA (27-mer)
8: RNA (27-mer)
BB: Coat protein
CC: Coat protein
DD: Coat protein
EE: Coat protein
FF: Coat protein
GG: Coat protein
HH: Coat protein
II: Coat protein
JJ: Coat protein
KK: Coat protein
LL: Coat protein
MM: Coat protein
NN: Coat protein
OO: Coat protein
PP: Coat protein
QQ: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
RR: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
SS: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
TT: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
UU: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
VV: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
WW: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
YY: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
ZZ: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
bb: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
cc: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
dd: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
ee: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
ff: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
gg: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
hh: RNA (27-mer)
ii: RNA (27-mer)
jj: RNA (27-mer)
kk: RNA (27-mer)
ll: RNA (27-mer)
mm: RNA (27-mer)
nn: RNA (27-mer)
oo: RNA (27-mer)
pp: RNA (27-mer)
qq: RNA (27-mer)
rr: RNA (27-mer)
ss: RNA (27-mer)
tt: RNA (27-mer)
uu: RNA (27-mer)
vv: RNA (27-mer)
ww: RNA (27-mer)
xx: RNA (27-mer)
yy: RNA (27-mer)
zz: RNA (27-mer)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,086,113115
Polymers1,085,543109
Non-polymers5706
Water28816
1
A: Coat protein
B: Coat protein
C: Coat protein
D: Coat protein
E: Coat protein
F: Coat protein
G: Coat protein
H: Coat protein
I: Coat protein
J: Coat protein
K: Coat protein
L: Coat protein
M: Coat protein
N: Coat protein
O: Coat protein
P: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
Q: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
R: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
S: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
T: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
U: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
V: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
W: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
X: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
Y: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
Z: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
a: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
b: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
c: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
d: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
e: RNA (27-mer)
f: RNA (27-mer)
g: RNA (27-mer)
h: RNA (27-mer)
i: RNA (27-mer)
j: RNA (27-mer)
k: RNA (27-mer)
l: RNA (27-mer)
m: RNA (27-mer)
n: RNA (27-mer)
o: RNA (27-mer)
p: RNA (27-mer)
q: RNA (27-mer)
r: RNA (27-mer)
s: RNA (27-mer)
t: RNA (27-mer)
u: RNA (27-mer)
v: RNA (27-mer)
w: RNA (27-mer)
x: RNA (27-mer)
y: RNA (27-mer)
z: RNA (27-mer)
1: RNA (27-mer)
2: RNA (27-mer)
3: RNA (27-mer)
4: RNA (27-mer)
5: RNA (27-mer)
6: RNA (27-mer)
7: RNA (27-mer)
8: RNA (27-mer)
BB: Coat protein
CC: Coat protein
DD: Coat protein
EE: Coat protein
FF: Coat protein
GG: Coat protein
HH: Coat protein
II: Coat protein
JJ: Coat protein
KK: Coat protein
LL: Coat protein
MM: Coat protein
NN: Coat protein
OO: Coat protein
PP: Coat protein
QQ: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
RR: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
SS: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
TT: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
UU: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
VV: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
WW: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
YY: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
ZZ: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
bb: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
cc: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
dd: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
ee: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
ff: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
gg: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
hh: RNA (27-mer)
ii: RNA (27-mer)
jj: RNA (27-mer)
kk: RNA (27-mer)
ll: RNA (27-mer)
mm: RNA (27-mer)
nn: RNA (27-mer)
oo: RNA (27-mer)
pp: RNA (27-mer)
qq: RNA (27-mer)
rr: RNA (27-mer)
ss: RNA (27-mer)
tt: RNA (27-mer)
uu: RNA (27-mer)
vv: RNA (27-mer)
ww: RNA (27-mer)
xx: RNA (27-mer)
yy: RNA (27-mer)
zz: RNA (27-mer)
hetero molecules

A: Coat protein
B: Coat protein
C: Coat protein
D: Coat protein
E: Coat protein
F: Coat protein
G: Coat protein
H: Coat protein
I: Coat protein
J: Coat protein
K: Coat protein
L: Coat protein
M: Coat protein
N: Coat protein
O: Coat protein
P: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
Q: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
R: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
S: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
T: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
U: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
V: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
W: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
X: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
Y: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
Z: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
a: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
b: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
c: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
d: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
e: RNA (27-mer)
f: RNA (27-mer)
g: RNA (27-mer)
h: RNA (27-mer)
i: RNA (27-mer)
j: RNA (27-mer)
k: RNA (27-mer)
l: RNA (27-mer)
m: RNA (27-mer)
n: RNA (27-mer)
o: RNA (27-mer)
p: RNA (27-mer)
q: RNA (27-mer)
r: RNA (27-mer)
s: RNA (27-mer)
t: RNA (27-mer)
u: RNA (27-mer)
v: RNA (27-mer)
w: RNA (27-mer)
x: RNA (27-mer)
y: RNA (27-mer)
z: RNA (27-mer)
1: RNA (27-mer)
2: RNA (27-mer)
3: RNA (27-mer)
4: RNA (27-mer)
5: RNA (27-mer)
6: RNA (27-mer)
7: RNA (27-mer)
8: RNA (27-mer)
BB: Coat protein
CC: Coat protein
DD: Coat protein
EE: Coat protein
FF: Coat protein
GG: Coat protein
HH: Coat protein
II: Coat protein
JJ: Coat protein
KK: Coat protein
LL: Coat protein
MM: Coat protein
NN: Coat protein
OO: Coat protein
PP: Coat protein
QQ: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
RR: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
SS: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
TT: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
UU: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
VV: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
WW: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
YY: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
ZZ: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
bb: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
cc: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
dd: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
ee: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
ff: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
gg: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
hh: RNA (27-mer)
ii: RNA (27-mer)
jj: RNA (27-mer)
kk: RNA (27-mer)
ll: RNA (27-mer)
mm: RNA (27-mer)
nn: RNA (27-mer)
oo: RNA (27-mer)
pp: RNA (27-mer)
qq: RNA (27-mer)
rr: RNA (27-mer)
ss: RNA (27-mer)
tt: RNA (27-mer)
uu: RNA (27-mer)
vv: RNA (27-mer)
ww: RNA (27-mer)
xx: RNA (27-mer)
yy: RNA (27-mer)
zz: RNA (27-mer)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,172,226230
Polymers2,171,086218
Non-polymers1,14012
Water46826
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
Unit cell
Length a, b, c (Å)192.08, 202.29, 177.93
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Space group name H-MP21212
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11a-165-

A

21a-165-

A

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Components

#1: Protein ...
Coat protein


Mass: 17533.949 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Source: (natural) Satellite tobacco mosaic virus / References: UniProt: P17574
#2: RNA chain ...
RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')


Mass: 5222.336 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Details: arbitrary RNA adenine nucleotide hexadecamer / Source: (natural) Satellite tobacco mosaic virus
#3: RNA chain ...
RNA (27-mer)


Mass: 8221.520 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Details: arbitrary RNA uridine nucleotide 27-mer / Source: (natural) Satellite tobacco mosaic virus
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.59 Å3/Da / Density % sol: 22.75 % / Description: small, thin, square plates
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Crystals were grown by sitting drop vapor diffusion in Cryschem plates using 0.6 ml reservoirs. The drops were 6 to 8 ul and composed of equal volumes of a 5 mg/ml virus stock solution ...Details: Crystals were grown by sitting drop vapor diffusion in Cryschem plates using 0.6 ml reservoirs. The drops were 6 to 8 ul and composed of equal volumes of a 5 mg/ml virus stock solution buffered with 0.1 M phosphate at pH 6.5, and the reservoir. The reservoirs were 16% ammonium sulfate buffered at pH 6.0 with 0.1 M phosphate. Crystallization was a room temperature.
PH range: 4.5 - 7.0

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 15, 1998 / Details: Osmic mirrors
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 4→70 Å / Num. obs: 48422 / % possible obs: 81.8 % / Redundancy: 6.8 % / Biso Wilson estimate: 26.66 Å2 / CC1/2: 0.94 / Rmerge(I) obs: 0.085 / Rsym value: 0.084 / Net I/σ(I): 5.6
Reflection shellResolution: 4→4.25 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 865 / CC1/2: 0.43 / Rsym value: 0.27 / % possible all: 36

-
Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NIA

4nia


Resolution: 4→60 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rwork0.2 --
obs-48359 81.8 %
Refinement stepCycle: LAST / Resolution: 4→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33540 13414 30 16 47000
LS refinement shellResolution: 4→4.08 Å / Rfactor Rfree: 0.3146 / Rfactor Rwork: 0.2475
Refinement TLS params.Method: refined / Origin x: 27.4346413481 Å / Origin y: 203.139221682 Å / Origin z: 45.4706307799 Å
111213212223313233
T0.204282342157 Å2-0.0186775042762 Å20.0195319187209 Å2-0.173423616784 Å2-0.002107005439 Å2--0.231560140557 Å2
L-0.141286199295 °20.00542631345253 °2-0.00613442623009 °2--0.0541210747534 °20.0402659001576 °2---0.0767455488548 °2
S0.000889236044593 Å °-0.018154854728 Å °0.00318322503122 Å °-0.0272549625425 Å °-0.0181258510992 Å °0.0620520429705 Å °0.0107028321799 Å °-0.0477984780403 Å °0.010135638531 Å °
Refinement TLS groupSelection details: all

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