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- PDB-1w8x: Structural analysis of PRD1 -

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Basic information

Entry
Database: PDB / ID: 1w8x
TitleStructural analysis of PRD1
Components
  • MAJOR CAPSID PROTEIN (PROTEIN P3)
  • PROTEIN P16
  • PROTEIN P30
  • PROTEIN P31
KeywordsVIRUS / P3 MAJOR CAPSID PROTEIN / P30 TAPE MEASURE / P31 PENTON PROTEIN / P16 MEMBRANE PROTEIN / VIRUS/VIRAL PROTEIN / ICOSAHEDRAL VIRUS
Function / homology
Function and homology information


viral inner membrane / virion component => GO:0044423 / viral capsid assembly / viral capsid / membrane => GO:0016020 / virion membrane
Similarity search - Function
Domain of unknown function (DUF1970) / Tectiviridae, minor capsid / Tectiviridae, minor capsid / Bacteriophage PRD1, P5, spike N-terminal / Bacteriophage PRD1, P5, spike N-terminal / Bacteriophage PRD1, P3 / Bacteriophage PRD1, P3, N-terminal / P3 major capsid protein / Group II dsDNA virus coat/capsid protein / Viral coat protein subunit
Similarity search - Domain/homology
Major capsid protein P3 / Penton protein P31 / Minor capsid protein P30 / Protein P16
Similarity search - Component
Biological speciesENTEROBACTERIA PHAGE PRD1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.2 Å
AuthorsAbrescia, N.G.A. / Cockburn, J.J.B. / Grimes, J.M. / Sutton, G.C. / Diprose, J.M. / Butcher, S.J. / Fuller, S.D. / San Martin, C. / Burnett, R.M. / Stuart, D.I. ...Abrescia, N.G.A. / Cockburn, J.J.B. / Grimes, J.M. / Sutton, G.C. / Diprose, J.M. / Butcher, S.J. / Fuller, S.D. / San Martin, C. / Burnett, R.M. / Stuart, D.I. / Bamford, D.H. / Bamford, J.K.H.
CitationJournal: Nature / Year: 2004
Title: Insights into assembly from structural analysis of bacteriophage PRD1.
Authors: Nicola G A Abrescia / Joseph J B Cockburn / Jonathan M Grimes / Geoffrey C Sutton / Jonathan M Diprose / Sarah J Butcher / Stephen D Fuller / Carmen San Martín / Roger M Burnett / David I ...Authors: Nicola G A Abrescia / Joseph J B Cockburn / Jonathan M Grimes / Geoffrey C Sutton / Jonathan M Diprose / Sarah J Butcher / Stephen D Fuller / Carmen San Martín / Roger M Burnett / David I Stuart / Dennis H Bamford / Jaana K H Bamford /
Abstract: The structure of the membrane-containing bacteriophage PRD1 has been determined by X-ray crystallography at about 4 A resolution. Here we describe the structure and location of proteins P3, P16, P30 ...The structure of the membrane-containing bacteriophage PRD1 has been determined by X-ray crystallography at about 4 A resolution. Here we describe the structure and location of proteins P3, P16, P30 and P31. Different structural proteins seem to have specialist roles in controlling virus assembly. The linearly extended P30 appears to nucleate the formation of the icosahedral facets (composed of trimers of the major capsid protein, P3) and acts as a molecular tape-measure, defining the size of the virus and cementing the facets together. Pentamers of P31 form the vertex base, interlocking with subunits of P3 and interacting with the membrane protein P16. The architectural similarities with adenovirus and one of the largest known virus particles PBCV-1 support the notion that the mechanism of assembly of PRD1 is scaleable and applies across the major viral lineage formed by these viruses.
History
DepositionOct 1, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 11, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Version format compliance
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MAJOR CAPSID PROTEIN (PROTEIN P3)
B: MAJOR CAPSID PROTEIN (PROTEIN P3)
C: MAJOR CAPSID PROTEIN (PROTEIN P3)
D: MAJOR CAPSID PROTEIN (PROTEIN P3)
E: MAJOR CAPSID PROTEIN (PROTEIN P3)
F: MAJOR CAPSID PROTEIN (PROTEIN P3)
G: MAJOR CAPSID PROTEIN (PROTEIN P3)
H: MAJOR CAPSID PROTEIN (PROTEIN P3)
I: MAJOR CAPSID PROTEIN (PROTEIN P3)
J: MAJOR CAPSID PROTEIN (PROTEIN P3)
K: MAJOR CAPSID PROTEIN (PROTEIN P3)
L: MAJOR CAPSID PROTEIN (PROTEIN P3)
M: PROTEIN P30
N: PROTEIN P31
P: PROTEIN P16


Theoretical massNumber of molelcules
Total (without water)557,10715
Polymers557,10715
Non-polymers00
Water0
1
A: MAJOR CAPSID PROTEIN (PROTEIN P3)
B: MAJOR CAPSID PROTEIN (PROTEIN P3)
C: MAJOR CAPSID PROTEIN (PROTEIN P3)
D: MAJOR CAPSID PROTEIN (PROTEIN P3)
E: MAJOR CAPSID PROTEIN (PROTEIN P3)
F: MAJOR CAPSID PROTEIN (PROTEIN P3)
G: MAJOR CAPSID PROTEIN (PROTEIN P3)
H: MAJOR CAPSID PROTEIN (PROTEIN P3)
I: MAJOR CAPSID PROTEIN (PROTEIN P3)
J: MAJOR CAPSID PROTEIN (PROTEIN P3)
K: MAJOR CAPSID PROTEIN (PROTEIN P3)
L: MAJOR CAPSID PROTEIN (PROTEIN P3)
M: PROTEIN P30
N: PROTEIN P31
P: PROTEIN P16
x 60


Theoretical massNumber of molelcules
Total (without water)33,426,409900
Polymers33,426,409900
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
A: MAJOR CAPSID PROTEIN (PROTEIN P3)
B: MAJOR CAPSID PROTEIN (PROTEIN P3)
C: MAJOR CAPSID PROTEIN (PROTEIN P3)
D: MAJOR CAPSID PROTEIN (PROTEIN P3)
E: MAJOR CAPSID PROTEIN (PROTEIN P3)
F: MAJOR CAPSID PROTEIN (PROTEIN P3)
G: MAJOR CAPSID PROTEIN (PROTEIN P3)
H: MAJOR CAPSID PROTEIN (PROTEIN P3)
I: MAJOR CAPSID PROTEIN (PROTEIN P3)
J: MAJOR CAPSID PROTEIN (PROTEIN P3)
K: MAJOR CAPSID PROTEIN (PROTEIN P3)
L: MAJOR CAPSID PROTEIN (PROTEIN P3)
M: PROTEIN P30
N: PROTEIN P31
P: PROTEIN P16
x 5


  • icosahedral pentamer
  • 2.79 MDa, 75 polymers
Theoretical massNumber of molelcules
Total (without water)2,785,53475
Polymers2,785,53475
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: MAJOR CAPSID PROTEIN (PROTEIN P3)
B: MAJOR CAPSID PROTEIN (PROTEIN P3)
C: MAJOR CAPSID PROTEIN (PROTEIN P3)
D: MAJOR CAPSID PROTEIN (PROTEIN P3)
E: MAJOR CAPSID PROTEIN (PROTEIN P3)
F: MAJOR CAPSID PROTEIN (PROTEIN P3)
G: MAJOR CAPSID PROTEIN (PROTEIN P3)
H: MAJOR CAPSID PROTEIN (PROTEIN P3)
I: MAJOR CAPSID PROTEIN (PROTEIN P3)
J: MAJOR CAPSID PROTEIN (PROTEIN P3)
K: MAJOR CAPSID PROTEIN (PROTEIN P3)
L: MAJOR CAPSID PROTEIN (PROTEIN P3)
M: PROTEIN P30
N: PROTEIN P31
P: PROTEIN P16
x 6


  • icosahedral 23 hexamer
  • 3.34 MDa, 90 polymers
Theoretical massNumber of molelcules
Total (without water)3,342,64190
Polymers3,342,64190
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
6
A: MAJOR CAPSID PROTEIN (PROTEIN P3)
B: MAJOR CAPSID PROTEIN (PROTEIN P3)
C: MAJOR CAPSID PROTEIN (PROTEIN P3)
D: MAJOR CAPSID PROTEIN (PROTEIN P3)
E: MAJOR CAPSID PROTEIN (PROTEIN P3)
F: MAJOR CAPSID PROTEIN (PROTEIN P3)
G: MAJOR CAPSID PROTEIN (PROTEIN P3)
H: MAJOR CAPSID PROTEIN (PROTEIN P3)
I: MAJOR CAPSID PROTEIN (PROTEIN P3)
J: MAJOR CAPSID PROTEIN (PROTEIN P3)
K: MAJOR CAPSID PROTEIN (PROTEIN P3)
L: MAJOR CAPSID PROTEIN (PROTEIN P3)
M: PROTEIN P30
N: PROTEIN P31
P: PROTEIN P16
x 60


  • crystal asymmetric unit, crystal frame
  • 33.4 MDa, 900 polymers
Theoretical massNumber of molelcules
Total (without water)33,426,409900
Polymers33,426,409900
Non-polymers00
Water0
TypeNameSymmetry operationNumber
transform to crystal frame1
point symmetry operation60
Unit cell
Length a, b, c (Å)903.000, 920.600, 926.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.327045, -0.944222, 0.038562), (0.927495, 0.312897, -0.204569), (0.181093, 0.102669, 0.978092)0.79425, -0.71734, -0.185
3generate(-0.761819, -0.600288, 0.243488), (0.556497, -0.798859, -0.228331), (0.331576, -0.038447, 0.942645)1.7242, -0.16728, -0.29576
4generate(-0.761819, 0.556497, 0.331576), (-0.600288, -0.798859, -0.038447), (0.243488, -0.228331, 0.942645)1.50469, 0.89001, -0.17922
5generate(0.327045, 0.927495, 0.181093), (-0.944222, 0.312897, 0.102669), (0.038562, -0.204569, 0.978092)0.43908, 0.99339, 0.00357
6generate(-0.870626, -0.139937, -0.471623), (-0.139937, -0.848637, 0.51013), (-0.471623, 0.51013, 0.719263)3.21129, -0.72726, 1.0967
7generate(-0.499933, 0.729857, -0.466237), (-0.740491, -0.081029, 0.667163), (0.449155, 0.678781, 0.580962)2.70743, -0.32401, 0.22311
8generate(0.429006, 0.652549, -0.624607), (-0.19651, 0.742332, 0.640568), (0.881668, -0.152066, 0.446697)1.87306, -0.97745, -0.01454
9generate(0.632428, -0.265024, -0.727872), (0.740244, 0.483589, 0.467099), (0.228198, -0.834209, 0.502018)1.86125, -1.78453, 0.71217
10generate(-0.170789, -0.754808, -0.633322), (0.775207, -0.499684, 0.386484), (-0.608182, -0.424949, 0.670473)2.68832, -1.62991, 1.39895
11generate(0.033243, -0.844772, 0.534092), (-0.844772, -0.30932, -0.43667), (0.534092, -0.43667, -0.723923)0.1994, 1.93403, 2.67328
12generate(-0.67593, -0.24088, 0.696488), (-0.642249, 0.656034, -0.396402), (-0.361434, -0.715259, -0.598139)0.73299, 1.56574, 3.54465
13generate(-0.318346, 0.634365, 0.704441), (0.326639, 0.770998, -0.546689), (-0.889923, 0.056061, -0.452652)0.24008, 0.65837, 3.88132
14generate(0.611826, 0.571404, 0.54696), (0.722921, -0.123305, -0.679839), (-0.32102, 0.811353, -0.488521)-0.59815, 0.46587, 3.21803
15generate(0.82912, -0.342753, 0.441679), (-0.001051, -0.790978, -0.611844), (0.55907, 0.506828, -0.656176)-0.62328, 1.25427, 2.47142
16generate(-0.162617, 0.98471, -0.062469), (0.98471, 0.157957, -0.07346), (-0.062469, -0.07346, -0.99534)1.50626, -1.03272, 3.91205
17generate(0.848817, 0.455245, -0.268813), (0.455245, -0.887902, -0.066191), (-0.268813, -0.066191, -0.960915)0.68229, -0.35034, 4.09927
18generate(0.651159, -0.686626, -0.323321), (-0.686626, -0.71447, 0.134451), (-0.323321, 0.134451, -0.936689)1.07963, 0.66041, 4.11102
19generate(-0.482435, -0.862877, -0.150665), (-0.862877, 0.438576, 0.251187), (-0.150665, 0.251187, -0.956141)2.14917, 0.6027, 3.93106
20generate(-0.985376, 0.170065, 0.01055), (0.170065, 0.977765, 0.12269), (0.01055, 0.12269, -0.992389)2.41284, -0.44371, 3.80809
21generate(-0.483322, -0.575459, -0.659733), (0.771511, 0.076158, -0.631641), (0.413727, -0.814277, 0.407164)3.11542, 0.3049, 0.66541
22generate(-0.811276, 0.20857, -0.546196), (0.20857, -0.769498, -0.603632), (-0.546196, -0.603632, 0.580774)3.26639, 0.97989, 1.5028
23generate(-0.170789, 0.775207, -0.608182), (-0.754808, -0.499684, -0.424949), (-0.633322, 0.386484, 0.670473)2.57347, 1.80921, 1.39455
24generate(0.553008, 0.341381, -0.760027), (-0.787266, 0.512727, -0.342526), (0.272755, 0.787763, 0.552299)1.99425, 1.64676, 0.49026
25generate(0.359852, -0.493377, -0.791888), (0.156051, 0.868617, -0.470269), (0.919867, 0.045652, 0.389565)2.32919, 0.71705, 0.03962
26generate(0.812466, 0.219441, -0.540134), (-0.384459, -0.494813, -0.779328), (-0.438282, 0.840836, -0.317653)1.25831, 2.03434, 3.03273
27generate(0.371428, -0.753941, -0.541862), (-0.725803, 0.128176, -0.675856), (0.579009, 0.644317, -0.499604)1.84612, 2.22811, 2.14023
28generate(-0.67593, -0.642249, -0.361434), (-0.24088, 0.656034, -0.715259), (0.696488, -0.396402, -0.598139)2.7822, 1.68473, 2.23034
29generate(-0.882195, 0.400162, -0.248197), (0.400162, 0.35928, -0.843083), (-0.248197, -0.843083, -0.477085)2.77292, 1.15513, 3.17853
30generate(0.037684, 0.932715, -0.35864), (0.311425, -0.351983, -0.882679), (-0.949523, -0.078427, -0.303735)1.8311, 1.3712, 3.67444
31generate(0.117706, 0.874383, 0.470743), (-0.376043, -0.39949, 0.836062), (0.919096, -0.275429, 0.281784)0.14244, -1.08252, 0.26154
32generate(0.93473, 0.210782, 0.286097), (-0.342103, 0.315907, 0.884968), (0.096155, -0.92508, 0.367397)-0.47839, -1.2493, 1.13697
33generate(0.553008, -0.787266, 0.272755), (0.341381, 0.512727, 0.787763), (-0.760027, -0.342526, 0.552299)0.05989, -1.91134, 1.80897
34generate(-0.499933, -0.740491, 0.449155), (0.729857, -0.081029, 0.678781), (-0.466237, 0.667163, 0.580962)1.01339, -2.15374, 1.34885
35generate(-0.768964, 0.286464, 0.571518), (0.286464, -0.64481, 0.708631), (0.571518, 0.708631, 0.413774)1.06441, -1.6415, 0.39249
36generate(-0.44685, -0.518365, 0.729124), (-0.011009, 0.818145, 0.574907), (-0.894541, 0.24887, -0.371295)0.40079, -1.08267, 3.72236
37generate(-0.494882, 0.334589, 0.801961), (0.859336, 0.325415, 0.39452), (-0.128968, 0.884395, -0.448567)0.28284, -1.78466, 2.90204
38generate(0.293711, 0.654307, 0.696861), (0.654307, -0.669077, 0.352445), (0.696861, 0.352445, -0.624633)-0.4986, -1.40855, 2.24818
39generate(0.82912, -0.001051, 0.55907), (-0.342753, -0.790978, 0.506828), (0.441679, -0.611844, -0.656176)-0.8636, -0.47411, 2.66439
40generate(0.371428, -0.725803, 0.579009), (-0.753941, 0.128176, 0.644317), (-0.541862, -0.675856, -0.499604)-0.30775, -0.27271, 3.57549
41generate(-0.483322, 0.771511, 0.413727), (-0.575459, 0.076158, -0.814277), (-0.659733, -0.631641, 0.407164)0.99522, 2.3114, 1.977
42generate(0.632428, 0.740244, 0.228198), (-0.265024, 0.483589, -0.834209), (-0.727872, 0.467099, 0.502018)-0.01863, 1.95035, 1.83078
43generate(0.93473, -0.342103, 0.096155), (0.210782, 0.315907, -0.92508), (0.286097, 0.884968, 0.367397)-0.08955, 1.54729, 0.82473
44generate(0.005813, -0.979763, 0.200078), (0.194412, -0.195156, -0.961311), (0.980903, 0.044485, 0.189343)0.88047, 1.65923, 0.34917
45generate(-0.870592, -0.291511, 0.396348), (-0.291511, -0.343329, -0.892831), (0.396348, -0.892831, 0.213921)1.5509, 2.13148, 1.06132
46generate(0.117706, -0.376043, 0.919096), (0.874383, -0.39949, -0.275429), (0.470743, 0.836062, 0.281784)-0.66422, -0.48497, 0.76431
47generate(-0.143842, -0.134441, 0.980426), (-0.134441, -0.978889, -0.153954), (0.980426, -0.153954, 0.122731)-0.47101, 0.54703, 0.48632
48generate(0.005813, 0.194412, 0.980903), (-0.979763, -0.195156, 0.044485), (0.200078, -0.961311, 0.189343)-0.6702, 1.17093, 1.35276
49generate(0.359852, 0.156051, 0.919867), (-0.493377, 0.868617, 0.045652), (-0.791888, -0.470269, 0.389565)-0.98651, 0.52452, 2.16623
50generate(0.429006, -0.19651, 0.881668), (0.652549, 0.742332, -0.152066), (-0.624607, 0.640568, 0.446697)-0.98281, -0.49888, 1.80254
51generate(-0.44685, -0.011009, -0.894541), (-0.518365, 0.818145, 0.24887), (0.729124, 0.574907, -0.371295)3.49698, 0.16715, 1.7123
52generate(-0.318346, 0.326639, -0.889923), (0.634365, 0.770998, 0.056061), (0.704441, -0.546689, -0.452652)3.31546, -0.87749, 1.94769
53generate(0.037684, 0.311425, -0.949523), (0.932715, -0.351983, -0.078427), (-0.35864, -0.882679, -0.303735)2.99293, -0.93708, 2.9831
54generate(0.129218, -0.035625, -0.990976), (-0.035625, -0.998876, 0.031264), (-0.990976, 0.031264, -0.130342)2.97513, 0.07072, 3.38762
55generate(-0.17024, -0.2349, -0.956995), (-0.932442, -0.275698, 0.233544), (-0.318701, 0.932101, -0.172096)3.28665, 0.75318, 2.60222
56generate(0.812466, -0.384459, -0.438282), (0.219441, -0.494813, 0.840836), (-0.540134, -0.779328, -0.317653)1.08898, -1.81954, 3.22843
57generate(-0.17024, -0.932442, -0.318701), (-0.2349, -0.275698, 0.932101), (-0.956995, 0.233544, -0.172096)2.09115, -1.44585, 3.41724
58generate(-0.978226, -0.163734, -0.127535), (-0.163734, 0.231231, 0.959022), (-0.127535, 0.959022, -0.253005)2.68377, -1.60709, 2.52145
59generate(-0.494882, 0.859336, -0.128968), (0.334589, 0.325415, 0.884395), (0.801961, 0.39452, -0.448567)2.04786, -2.08043, 1.77902
60generate(0.611826, 0.722921, -0.32102), (0.571404, -0.123305, 0.811353), (0.54696, -0.679839, -0.488521)1.06223, -2.21173, 2.21595

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Components

#1: Protein
MAJOR CAPSID PROTEIN (PROTEIN P3)


Mass: 43477.414 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) ENTEROBACTERIA PHAGE PRD1 (virus) / Strain: SUS539 MUTANT / References: UniProt: P22535
#2: Protein PROTEIN P30 / PROTEIN P / GPP


Mass: 9061.300 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ENTEROBACTERIA PHAGE PRD1 (virus) / Strain: SUS539 MUTANT / References: UniProt: P27391
#3: Protein PROTEIN P31 / PROTEIN C / GPC


Mass: 13757.388 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ENTEROBACTERIA PHAGE PRD1 (virus) / Strain: SUS539 MUTANT / References: UniProt: P27384
#4: Protein PROTEIN P16 / PROTEIN S / GPS


Mass: 12559.167 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ENTEROBACTERIA PHAGE PRD1 (virus) / Strain: SUS539 MUTANT / References: UniProt: P27392

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1000

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Sample preparation

CrystalDescription: MOLECULAR REPLACEMENT MODEL BASED ON HYBRID STRUCTURE OF EM RECONSTRUCTION OF PRD1 WITH FITTED HIGH RESOLUTION CRYSTAL STRUCTURE OF P3
Crystal growpH: 7.2
Details: 3.7 W/V PEG 8000, 400 MM NACL 100 MM POTASSIUM PHOSPHATE BUFFER PH 7.2

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Data collection

DiffractionMean temperature: 278 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.99
DetectorType: ADSC CCD / Detector: CCD / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 4.2→100 Å / Num. obs: 2383561 / % possible obs: 45 % / Observed criterion σ(I): -5 / Redundancy: 1.6 % / Rmerge(I) obs: 0.33 / Net I/σ(I): 1.8
Reflection shellResolution: 4.2→4.27 Å / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 0.9 / % possible all: 7

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Processing

Software
NameClassification
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.2→100 Å / Num. reflection obs: 2383561
Details: THE MODEL WAS BUILT INTO A 60-FOLD AVERAGED ELECTRON DENSITY MAP (OVERALL RECIPROCAL SPACE CORRELATION COEFFICIENT 0.90). PROTEINS P3 WERE BASED ON A HIGH RESOLUTION REFINED X-RAY STRUCTURE, ...Details: THE MODEL WAS BUILT INTO A 60-FOLD AVERAGED ELECTRON DENSITY MAP (OVERALL RECIPROCAL SPACE CORRELATION COEFFICIENT 0.90). PROTEINS P3 WERE BASED ON A HIGH RESOLUTION REFINED X-RAY STRUCTURE, POSITIONED IN THE VIRION BY RIGID BODY REFINEMENT USING XPLOR3.1. THE REGIONS OF THE P3 MOLECULES SHOWING CONFORMATIONAL CHANGES WERE REMODELLED USING O. PROTEINS P16,P30 & P31 WERE MODELLED AB INITIO USING O AND C-ALPHA TO IMPOSE REASONABLE STEREOCHEMISTRY. DUE TO THE LIMITED RESOLUTION OF THE DATA THE MODEL WAS NOT SUBJECTED TO FURTHER CONVENTIONAL REFINEMENT.
Refinement stepCycle: LAST / Resolution: 4.2→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms38116 0 0 0 38116

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