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- PDB-1qjy: HUMAN RHINOVIRUS 16 COAT PROTEIN IN COMPLEX WITH ANTIVIRAL COMPOU... -

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Basic information

Entry
Database: PDB / ID: 1qjy
TitleHUMAN RHINOVIRUS 16 COAT PROTEIN IN COMPLEX WITH ANTIVIRAL COMPOUND VP65099
Components
  • PROTEIN VP1
  • PROTEIN VP2
  • PROTEIN VP3
  • PROTEIN VP4
KeywordsVIRUS / NUCLEOTIDYLTRANSFERASE / RHINOVIRUS COAT PROTEIN / RNA-BINDING / TRANSFERASE / LIPOPROTEIN / WIN COMPOUND / PHOSPHOPROTEIN / THIOL PROTEASE / CAPSID PROTEIN / DRUG / VIRION / MEMBRANE / HELICASE / PROTEASE / NUCLEOTIDE-BINDING / HUMAN RHINOVIRUS 16 / RNA REPLICATION / ANTIVIRAL COMPOUND / COVALENT PROTEIN-RNA LINKAGE / MYRISTATE / HYDROLASE / CYTOPLASM / ATP-BINDING / CYTOPLASMIC VESICLE / HOST-VIRUS INTERACTION / RNA-DIRECTED RNA POLYMERASE
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / ribonucleoside triphosphate phosphatase activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / ribonucleoside triphosphate phosphatase activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / symbiont-mediated suppression of host gene expression / DNA replication / RNA helicase activity / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / : / host cell nucleus / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
Jelly Rolls - #20 / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) ...Jelly Rolls - #20 / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / Jelly Rolls / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
MYRISTIC ACID / Chem-W03 / Genome polyprotein
Similarity search - Component
Biological speciesHUMAN RHINOVIRUS 16
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHadfield, A.T. / Diana, G.D. / Rossmann, M.G.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Analysis of Three Structurally Related Antiviral Compounds in Complex with Human Rhinovirus 16
Authors: Hadfield, A.T. / Minor, I. / Diana, G.D. / Rossmann, M.G.
#1: Journal: Structure / Year: 1997
Title: The Refined Structure of Human Rhinovirus 16 at 2.15 Angstroms Resolution: Implications for the Viral Life Cycle
Authors: Hadfield, A.T. / Lee, W.M. / Zhao, R. / Oliveira, M.A. / Minor, I. / Rueckert, R.R. / Rossmann, M.G.
#2: Journal: Structure / Year: 1993
Title: The Structure of Human Rhinovirus 16
Authors: Oliveira, M.A. / Zhao, R. / Lee, W.M. / Kremer, M.J. / Minor, I. / Rueckert, R.R. / Diana, G.D. / Pevear, D.C. / Dutko, F.J. / Mckinlay, M.A. / Rossmann, M.G.
#3: Journal: J.Mol.Biol. / Year: 1993
Title: A Comparison of the Anti-Rhinoviral Drug Binding Pocket in Hrv14 and Hrv1A
Authors: Kim, K.H. / Willingmann, P. / Gong, Z.X. / Kremer, M.J. / Chapman, M.S. / Minor, I. / Oliveira, M.A. / Rossmann, M.G. / Andries, K. / Diana, G.D. / Dutko, F.J. / Mckinlay, M.A. / Pevear, D.C.
#4: Journal: J.Mol.Biol. / Year: 1989
Title: Crystal Structure of Human Rhinovirus Serotype 1A (Hrv1A)
Authors: Kim, S.S. / Smith, T.J. / Chapman, M.S. / Rossmann, M.G. / Pevear, D.C. / Dutko, F.J. / Felock, P.J. / Diana, G.D. / Mckinlay, M.A.
#5: Journal: Science / Year: 1986
Title: The Site of Attachment in Human Rhinovirus 14 for Antiviral Agents that Inhibit Uncoating
Authors: Smith, T.J. / Kremer, M.J. / Luo, M. / Vriend, G. / Arnold, E. / Kamer, G. / Rossmann, M.G. / Mckinlay, M.A. / Diana, G.D. / Otto, M.J.
#6: Journal: Nature / Year: 1985
Title: Structure of a Human Common Cold Virus and Functional Relationship to Other Picornaviruses
Authors: Rossmann, M.G. / Arnold, E. / Erickson, J.W. / Frankenberger, E.A. / Griffith, J.P. / Hecht, H.J. / Johnson, J.E. / Kamer, G. / Luo, M. / Mosser, A.G. / Rueckert, R.R. / Sherry, B. / Vriend, G.
History
DepositionJul 6, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 1999Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 285 THE VIRION IS ORIENTED WITH ITS TWO FOLD ALONG THE CRYSTALLOGRAPHIC TWO FOLD AXIS IN P 2 21 21. ... THE VIRION IS ORIENTED WITH ITS TWO FOLD ALONG THE CRYSTALLOGRAPHIC TWO FOLD AXIS IN P 2 21 21. SPACE GROUP P 2 21 21 WAS USED SO THAT THE VIRAL TWO-FOLD COINCIDES WITH THE X AXIS. THE COORDINATES ARE IN THE P,Q,R FRAME IN ANGSTROM UNITS AND CORRESPOND TO ICOSAHEDRAL SYMMETRY AXES. THE ORIGIN IS CHOSEN AT THE CENTRE OF THE VIRUS WITH P, Q AND R ALONG MUTUALLY PERPENDICULAR TWO-FOLD AXES OF THE ICOSAHEDRON. THEY SHOULD REMAIN IN THAT FRAME FOR THE EASE OF THE USER IN CREATING THE BIOLOGICALLY SIGNIFICANT VIRAL PARTICLE USING THE 60 ICOSAHEDRAL SYMMETRY OPERATORS. THE GIVEN ORIGX PUTS THE CENTRE OF THE VIRION AT THE ORIGIN, WITH A NON CRYSTALLOGRAPHIC TWO FOLD AXIS ALONG X TO CORRESPOND TO THE CRYSTALLOGRAPHIC TWO FOLD. THE ORIENTATION CORRESPONDS TO THAT GIVEN IN OTHER RHINOVIRUS STRUCTURES.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: PROTEIN VP1
2: PROTEIN VP2
3: PROTEIN VP3
4: PROTEIN VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,8007
Polymers95,1804
Non-polymers6203
Water5,459303
1
1: PROTEIN VP1
2: PROTEIN VP2
3: PROTEIN VP3
4: PROTEIN VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,748,021420
Polymers5,710,811240
Non-polymers37,210180
Water4,324240
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
1: PROTEIN VP1
2: PROTEIN VP2
3: PROTEIN VP3
4: PROTEIN VP4
hetero molecules
x 5


  • icosahedral pentamer
  • 479 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)479,00235
Polymers475,90120
Non-polymers3,10115
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
1: PROTEIN VP1
2: PROTEIN VP2
3: PROTEIN VP3
4: PROTEIN VP4
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 575 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)574,80242
Polymers571,08124
Non-polymers3,72118
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
6
1: PROTEIN VP1
2: PROTEIN VP2
3: PROTEIN VP3
4: PROTEIN VP4
hetero molecules
x 30


  • crystal asymmetric unit, crystal frame
  • 2.87 MDa, 120 polymers
Theoretical massNumber of molelcules
Total (without water)2,874,011210
Polymers2,855,405120
Non-polymers18,60590
Water2,162120
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation29
Unit cell
Length a, b, c (Å)362.600, 347.100, 334.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.499997, -0.361145, -0.787139), (-0.255564, 0.806893, -0.532559), (0.827459, 0.467422, 0.311144)45.32367, 23.16601, -75.00642
3generate(-0.309032, -0.839903, -0.446149), (-0.774664, 0.494442, -0.394257), (0.551729, 0.223763, -0.803444)118.65952, 70.22075, -50.01245
4generate(-0.309037, -0.774647, 0.551732), (-0.839922, 0.494444, 0.223778), (-0.446139, -0.394249, -0.803441)118.65991, 76.13617, 40.44108
5generate(0.49999, -0.255558, 0.827468), (-0.361153, 0.806896, 0.467442), (-0.787127, -0.532542, 0.311148)45.32429, 32.73736, 71.35048
6generate(-0.809027, -0.478748, 0.34097), (-0.478769, 0.200218, -0.854807), (0.340987, -0.854816, -0.391191)163.98236, 43.39881, -30.90939
7generate(-2.2E-5, 0.065254, 0.997868), (-0.997869, -0.065097, 0.004261), (0.065258, -0.995743, 0.065119)90.64871, 90.45356, -5.91543
8generate(0.809007, 0.519087, 0.275747), (-0.478769, 0.309841, 0.821455), (0.340987, -0.796588, 0.499186)17.31285, 43.39882, -30.90939
9generate(0.50001, 0.255569, -0.827448), (0.361153, 0.80688, 0.46744), (0.787127, -0.532577, 0.311144)45.32244, -32.73736, -71.35048
10generate(-0.49999, -0.361127, -0.787138), (0.361153, 0.739129, -0.568548), (0.787127, -0.568564, -0.239139)135.96918, -32.73736, -71.35048
11generate(0.309037, 0.839905, 0.446142), (0.839922, -0.461089, 0.28626), (0.446139, 0.286252, -0.847948)62.63356, -76.13617, -40.44109
12generate(0.309032, 0.774644, -0.551739), (0.774664, -0.541579, -0.32651), (-0.551729, -0.326496, -0.767454)62.63395, -70.22075, 50.01245
13generate(-0.499997, 0.255554, -0.827465), (0.255564, -0.86938, -0.422937), (-0.827459, -0.422918, 0.369377)135.9698, -23.16601, 75.00642
14generate(-1, 1.0E-6, 8.0E-6), (-0.991483, 0.130238), (0.130238, 0.991483)181.29347, 1.0E-5
15generate(-0.49999, 0.361149, 0.787141), (0.361153, -0.739145, 0.568546), (0.787127, 0.568529, 0.239135)135.96919, -32.73735, -71.35048
16generate(-4.0E-6, 0.997867, -0.06528), (-0.065258, -0.065117, -0.995741), (-0.997869, 0.004281, 0.065122)90.64712, 5.91542, 90.45354
17generate(-0.309037, 0.77466, -0.551731), (-0.839922, -0.494407, -0.223773), (-0.446139, 0.394269, 0.803444)118.65991, 76.13618, 40.44109
18generate(-0.809027, 0.478784, -0.340965), (-0.478769, -0.200197, 0.85481), (0.340987, 0.854801, 0.391189)163.98235, 43.39882, -30.90939
19generate(-0.809005, 0.519129, 0.275746), (0.5191, 0.410925, 0.749443), (0.275729, 0.749438, -0.60192)163.98038, -47.05474, -24.99397
20generate(-0.309002, 0.839939, 0.446129), (0.774664, 0.494408, -0.394261), (-0.551729, 0.223787, -0.803441)118.65671, -70.22075, 50.01245
21generate(0.809005, -0.478795, 0.341001), (-0.5191, -0.309819, 0.796582), (-0.275729, -0.821447, -0.499186)17.31309, 47.05475, 24.99396
22generate(0.809027, -0.519113, -0.275712), (0.478769, 0.30982, 0.821452), (-0.340987, -0.796573, 0.499188)17.31112, -43.39881, 30.9094
23generate(0.309037, -0.839919, -0.446144), (0.839922, 0.461052, -0.286265), (0.446139, -0.286272, 0.847945)62.63357, -76.13617, -40.44108
24generate(4.0E-6, -0.997869, 0.065236), (0.065258, -0.06512, -0.995742), (0.997869, 0.004237, 0.065116)90.64635, -5.91542, -90.45354
25generate(0.309001, -0.774683, 0.551719), (-0.774664, -0.541545, -0.326506), (0.551729, -0.32652, -0.767457)62.63676, 70.22076, -50.01245
26generate(-0.499997, -0.255532, 0.827468), (0.255564, 0.869369, 0.422936), (-0.827459, 0.422954, -0.369372)135.96981, -23.16601, 75.00641
27generate(0.500003, 0.361161, 0.787114), (0.255564, 0.806882, -0.53256), (-0.827459, 0.467459, 0.311149)45.32307, -23.16601, 75.00641
28generate(0.809005, 0.47876, -0.341006), (-0.5191, 0.309842, -0.796579), (-0.275729, 0.82146, 0.499188)17.31309, 47.05474, 24.99396
29generate(-2.2E-5, -0.065254, -0.997868), (-0.997869, 0.065141, -0.004256), (0.065258, 0.99574, -0.065119)90.64871, 90.45356, -5.91543
30generate(-0.809029, -0.519071, -0.275712), (-0.5191, 0.410948, 0.749446), (-0.275729, 0.74945, -0.601918)163.98259, 47.05475, 24.99396

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Components

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Protein , 4 types, 4 molecules 1234

#1: Protein PROTEIN VP1 / VIRION PROTEIN 1 / P1D / HUMAN RHINOVIRUS 16 COAT PROTEIN


Mass: 32501.375 Da / Num. of mol.: 1 / Fragment: RESIDUES 569-853 / Source method: isolated from a natural source / Source: (natural) HUMAN RHINOVIRUS 16 / Strain: SEROTYPE 16 / References: UniProt: Q82122
#2: Protein PROTEIN VP2 / VIRION PROTEIN 2 / P1B / HUMAN RHINOVIRUS 16 COAT PROTEIN


Mass: 28990.615 Da / Num. of mol.: 1 / Fragment: RESIDUES 70-330 / Source method: isolated from a natural source / Source: (natural) HUMAN RHINOVIRUS 16 / Strain: SEROTYPE 16 / References: UniProt: Q82122
#3: Protein PROTEIN VP3 / VIRION PROTEIN 3 / P1C / HUMAN RHINOVIRUS 16 COAT PROTEIN


Mass: 26314.168 Da / Num. of mol.: 1 / Fragment: RESIDUES 331-568 / Source method: isolated from a natural source / Source: (natural) HUMAN RHINOVIRUS 16 / Strain: SEROTYPE 16 / References: UniProt: Q82122
#4: Protein PROTEIN VP4 / VIRION PROTEIN 4 / P1A / HUMAN RHINOVIRUS 16 COAT PROTEIN


Mass: 7374.025 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-69 / Source method: isolated from a natural source
Details: RESIDUE 1 OF CHAIN 4 MYRISTOYLATED (RESIDUE 4000 IS MYRISTATE) ANTIVIRAL COMPOUND VP61209 (FORMERLY WIN 61209) LOCATED IN A POCKET IN VIRAL PROTEIN WITH A POSSIBLE ZINC, LOCATED ON FIVE FOLD AXES
Source: (natural) HUMAN RHINOVIRUS 16 / Strain: SEROTYPE 16 / References: UniProt: Q82122

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Non-polymers , 4 types, 306 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-W03 / 2,6-DIMETHYL-1-(3-[3-METHYL-5-ISOXAZOLYL]-PROPANYL)-4-[2-METHYL-4-ISOXAZOLYL]-PHENOL / WIN65099


Mass: 326.390 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H22N2O3
#7: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 9

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50 %
Description: ALTHOUGH OVERALL COMPLETENESS IS LOW (58.7%) THE PRESENCE OF 30-FOLD NON-CRYSTALLOGRAPHIC SYMMETRY GIVES A DATA -TO-PARAMETER RATIO OF 22:1
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: VIRUS WAS CRYSTALLISED USING THE HANGING DROP METHOD. 5 MICROLITERS OF VIRUS SOLUTION IN 0.25M HEPES BUFFER (PH 7.5), WITH 0.25M NACL WAS MIXED WITH 5 MICROLITERS OF THE RESERVOIR SOLUTION, 0.5-1.5% PEG 8000.
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18-10 mg/mlprotein1drop
20.25 mMHEPES1drop
30.5-1.5 %PEG80001drop
40.5-1.5 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.91
DetectorType: KODAK FILM / Detector: FILM / Date: Apr 15, 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 416368 / % possible obs: 36.9 % / Observed criterion σ(I): 3 / Redundancy: 1.3 % / Rmerge(I) obs: 0.11
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.154 / % possible all: 32.6
Reflection shell
*PLUS
% possible obs: 32.6 %

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
PURDUEDATA PROCESSING PACKAGEdata reduction
PURDUEDATA PROCESSING PACKAGEdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AYM

1aym


Resolution: 2.8→30 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.01 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Details: BULK SOLVENT CORRECTION APPLIED DISORDERED SIDE CHAINS (2 159, 2 160) WERE MODELLED WITH PREFERRED ROTAMERS WITH GOOD STEREO CHEMISTRY. IN CHAIN 2, RESIDUES 159 AND 160 SIDE CHAINS WERE NOT ...Details: BULK SOLVENT CORRECTION APPLIED DISORDERED SIDE CHAINS (2 159, 2 160) WERE MODELLED WITH PREFERRED ROTAMERS WITH GOOD STEREO CHEMISTRY. IN CHAIN 2, RESIDUES 159 AND 160 SIDE CHAINS WERE NOT VISIBLE IN THE ELECTRON DENSITY MAPS, AND SIDE CHAIN ATOMS WERE INCLUDED USING A LIKELY ROTAMER. FOR CHAIN 4, RESIDUES 8 TO 22 WERE NOT OBSERVED.
RfactorNum. reflection% reflectionSelection details
Rfree0.233 3318 1 %RANDOM
Rwork0.233 ---
obs0.233 391133 38.4 %-
Displacement parametersBiso mean: 20.2 Å2
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6336 0 40 303 6679
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.2
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.51.5
X-RAY DIFFRACTIONx_mcangle_it1.52
X-RAY DIFFRACTIONx_scbond_it22
X-RAY DIFFRACTIONx_scangle_it22.5
LS refinement shellResolution: 2.8→2.93 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.29 552 1 %
Rwork0.295 38038 -
obs--44.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2WINPAR.AHHRV16TOP.AH
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.2

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