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- PDB-4g93: CRYSTAL STRUCTURE OF THE HUMAN HEPATITIS B VIRUS T = 4 CAPSID, AD... -

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Basic information

Entry
Database: PDB / ID: 4g93
TitleCRYSTAL STRUCTURE OF THE HUMAN HEPATITIS B VIRUS T = 4 CAPSID, ADYW STRAIN, in COMPLEX WITH THE PHENYLPROPENAMIDE ASSEMBLY ACCELERATOR AT-130
ComponentsCapsid protein
Keywordsvirus/inhibitor / VIRUS / CAPSID / HEPADNAVIRUS / ICOSAHEDRAL / ASSEMBLY EFFECTOR / ASSEMBLY ACCELERATOR / KINETIC EFFECTOR / PHENYLPROPENAMIDE / virus-inhibitor complex
Function / homology
Function and homology information


microtubule-dependent intracellular transport of viral material towards nucleus / T=4 icosahedral viral capsid / viral penetration into host nucleus / host cell / host cell cytoplasm / symbiont entry into host cell / structural molecule activity / DNA binding / RNA binding / identical protein binding
Similarity search - Function
Hepatitis core antigen / Viral capsid core domain supefamily, Hepatitis B virus / Hepatitis core antigen
Similarity search - Domain/homology
Chem-0YP / Capsid protein
Similarity search - Component
Biological speciesHepatitis B virus subtype adyw
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4.2 Å
AuthorsKaten, S.P. / Zlotnick, A.
CitationJournal: Structure / Year: 2013
Title: Assembly-directed antivirals differentially bind quasiequivalent pockets to modify hepatitis B virus capsid tertiary and quaternary structure.
Authors: Katen, S.P. / Tan, Z. / Chirapu, S.R. / Finn, M.G. / Zlotnick, A.
History
DepositionJul 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Feb 28, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsid protein
B: Capsid protein
C: Capsid protein
D: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1416
Polymers67,1644
Non-polymers9772
Water00
1
A: Capsid protein
B: Capsid protein
C: Capsid protein
D: Capsid protein
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)4,088,465360
Polymers4,029,865240
Non-polymers58,600120
Water0
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
A: Capsid protein
B: Capsid protein
C: Capsid protein
D: Capsid protein
hetero molecules
x 5


  • icosahedral pentamer
  • 341 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)340,70530
Polymers335,82220
Non-polymers4,88310
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein
B: Capsid protein
C: Capsid protein
D: Capsid protein
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 409 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)408,84636
Polymers402,98624
Non-polymers5,86012
Water0
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
A: Capsid protein
B: Capsid protein
C: Capsid protein
D: Capsid protein
hetero molecules
x 60


  • crystal asymmetric unit, crystal frame
  • 4.09 MDa, 240 polymers
Theoretical massNumber of molelcules
Total (without water)4,088,465360
Polymers4,029,865240
Non-polymers58,600120
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
Unit cell
Length a, b, c (Å)527.379, 362.754, 538.226
Angle α, β, γ (deg.)90.00, 105.13, 90.00
Int Tables number5
Space group name H-MC121
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1generate(1), (1), (1)
2generate(-0.961626, 0.096177, 0.256908), (0.096213, -0.758885, 0.644057), (0.257025, 0.644107, 0.720511)156.27783, -92.99033, 11.46591
3generate(0.976098, -0.1172, -0.182989), (0.211212, 0.312304, 0.926148), (-0.05142, -0.942779, 0.329638)26.08829, -140.76361, 92.07757
4generate(0.497937, 0.801101, -0.332083), (-0.378428, 0.545325, 0.747865), (0.780297, -0.246808, 0.574778)91.69246, -60.5882, -20.19032
5generate(0.383492, -0.158625, -0.90975), (0.552312, 0.828942, 0.088276), (0.740224, -0.536388, 0.405606)177.81903, -64.87083, 5.66599
6generate(0.452899, 0.047763, -0.890207), (-0.570229, 0.783142, -0.248115), (0.685356, 0.620067, 0.381999)168.56886, 87.37247, 14.03845
7generate(-0.738099, 0.366532, -0.566479), (0.366463, -0.487141, -0.792641), (-0.566467, -0.792772, 0.22524)241.65604, 67.56316, 155.44019
8generate(-0.499967, -0.71521, -0.488369), (0.724708, -0.036808, -0.687977), (0.474213, -0.697961, 0.536775)208.48264, 19.32635, 14.34141
9generate(0.559465, -0.811238, -0.170024), (0.425764, 0.457306, -0.780696), (0.711168, 0.364459, 0.601268)64.68591, 60.2775, -16.9487
10generate(-0.499937, 0.724763, 0.474074), (-0.715252, -0.036783, -0.697889), (-0.488364, -0.688114, 0.536719)83.42107, 159.83711, 107.41571
11generate(0.9761, 0.211152, -0.051397), (-0.117244, 0.312344, -0.942659), (-0.183065, 0.926264, 0.329596)8.98925, 133.8237, 104.8111
12generate(0.366054, -0.91213, -0.184493), (0.90978, 0.309022, 0.277135), (-0.19574, -0.269281, 0.942964)85.26595, -123.97284, 26.33631
13generate(-0.948254, -0.251603, 0.193622), (-0.251669, 0.223557, -0.941599), (0.193695, -0.941705, -0.275303)163.20828, 146.68277, 146.98369
14generate(-0.153311, -0.886805, 0.435973), (-0.122303, -0.4208, -0.898814), (0.980647, -0.191113, -0.043928)54.85843, 128.61569, 40.83264
15generate(0.383575, 0.552313, 0.74012), (-0.158677, 0.828966, -0.53632), (-0.909856, 0.088279, 0.405499)-36.57113, 85.0304, 165.21828
16generate(0.498022, -0.378493, 0.780207), (0.801063, 0.545323, -0.246714), (-0.332114, 0.747993, 0.574695)-52.84525, -45.39316, 87.37408
17generate(-0.153293, -0.122276, 0.980529), (-0.886784, -0.4208, -0.191115), (0.436028, -0.898943, -0.043947)-15.90229, 110.57215, 93.4917
18generate(-0.125483, 0.094465, 0.987527), (0.094503, -0.989796, 0.106712), (0.987652, 0.106683, 0.115279)-19.50038, -23.00299, 19.46814
19generate(0.453001, -0.570234, 0.685304), (0.047776, 0.783115, 0.619991), (-0.890306, -0.248092, 0.381923)-36.16088, -85.18012, 166.39149
20generate(-0.487099, -0.773949, 0.404608), (0.608589, 0.031466, 0.792837), (-0.626363, 0.632563, 0.455633)91.20624, -161.8618, 131.2943
21generate(-0.487183, 0.608577, -0.626347), (-0.773897, 0.031493, 0.63243), (0.40468, 0.792894, 0.45569)225.17528, -7.35276, 31.60031
22generate(0.174137, -0.153832, -0.972565), (0.939044, -0.271393, 0.211072), (-0.296421, -0.950157, 0.097256)206.2225, -118.21809, 145.96092
23generate(-0.659729, -0.566075, -0.494284), (0.559921, -0.80897, 0.179126), (-0.501215, -0.158599, 0.850659)224.69783, -77.41145, 67.86526
24generate(0.174157, 0.93905, -0.296416), (-0.153893, -0.271352, -0.950036), (-0.972685, 0.211056, 0.097195)118.36275, 138.3257, 211.35352
25generate(0.672328, -0.292743, 0.679922), (0.504886, -0.490391, -0.710273), (0.541361, 0.820932, -0.181937)-56.66711, 43.47691, 101.23779
26generate(-0.359282, -0.162002, 0.91899), (-0.670033, 0.730291, -0.133229), (-0.649621, -0.663669, -0.371009)12.01013, 82.09393, 240.95576
27generate(0.735043, -0.431487, 0.523047), (-0.431447, -0.892707, -0.130062), (0.523008, -0.130064, -0.842336)-42.34658, 58.61461, 188.82355
28generate(0.387659, 0.709613, 0.588345), (0.763145, 0.110952, -0.636541), (-0.517078, 0.695826, -0.498611)-17.24448, 8.9265, 244.72133
29generate(-0.613914, 0.73504, 0.287793), (0.295565, 0.552192, -0.779504), (-0.731949, -0.393548, -0.556319)118.64615, 72.71099, 272.99463
30generate(0.937416, 0.22445, -0.266148), (0.021508, -0.800347, -0.599103), (-0.347629, 0.55595, -0.755109)40.63382, 75.76723, 261.66714
31generate(-0.225867, -0.944639, 0.238022), (-0.944637, 0.152693, -0.29045), (0.237996, -0.290419, -0.926826)87.59499, 129.07315, 227.35854
32generate(0.599441, -0.714017, -0.361712), (-0.60299, -0.105611, -0.790701), (0.526343, 0.69222, -0.49383)85.72853, 161.04295, 143.21671
33generate(0.286447, 0.180119, -0.940949), (-0.877265, -0.345497, -0.333217), (-0.385201, 0.92102, 0.05905)191.25572, 128.11638, 159.50912
34generate(-0.659749, 0.559929, -0.501259), (-0.566078, -0.808944, -0.158589), (-0.494265, 0.179096, 0.850653)225.60609, 75.33828, 67.19409
35generate(-0.359364, -0.670009, -0.649546), (-0.162039, 0.730291, -0.66362), (0.919092, -0.133205, -0.370927)215.8316, 101.89679, 89.2739
36generate(-0.617858, -0.428711, -0.659123), (-0.428672, -0.519094, 0.73938), (-0.659174, 0.739504, 0.136952)242.06854, -54.62783, 175.87579
37generate(-0.458889, 0.445249, -0.768883), (0.030204, 0.872711, 0.487255), (0.888062, 0.200384, -0.413822)240.96068, -66.23356, 97.84772
38generate(-0.432229, -0.492947, -0.755083), (-0.874869, 0.432223, 0.218536), (0.218625, 0.755194, -0.618034)236.5898, 56.19067, 189.10745
39generate(-0.613965, 0.29565, -0.731882), (0.734986, 0.552178, -0.393486), (0.287856, -0.779611, -0.556252)251.14635, -19.93328, 174.38603
40generate(0.11416, 0.05552, -0.991853), (0.055518, -0.997234, -0.049426), (-0.991976, -0.049434, -0.116926)214.52766, 1.05456, 241.04131
41generate(0.937415, 0.021519, -0.347483), (0.224503, -0.800372, 0.555883), (-0.266261, -0.599181, -0.755083)51.20249, -93.93685, 253.79672
42generate(-0.432166, -0.87489, 0.21864), (-0.492921, 0.432207, 0.755049), (-0.755191, 0.218648, -0.618081)110.0594, -50.45188, 283.26715
43generate(-0.499208, 0.854288, 0.144913), (0.854269, 0.457274, 0.247197), (0.144914, 0.247204, -0.958067)126.12141, -114.71569, 240.41766
44generate(-0.988677, -0.149986, 0.004326), (-0.15002, 0.987031, -0.057286), (0.004324, -0.057249, -0.998353)191.71352, 21.94842, 259.24536
45generate(0.366021, 0.909786, -0.195773), (-0.912128, 0.309064, -0.26929), (-0.184501, 0.277111, 0.942955)86.73479, 123.18047, 25.25092
46generate(0.187493, 0.848462, -0.49493), (0.848424, -0.393808, -0.353607), (-0.495021, -0.353688, -0.793685)142.86798, -36.08281, 280.93036
47generate(0.430736, -0.754822, -0.494639), (-0.754782, -0.601795, 0.260946), (-0.494786, 0.261038, -0.828941)119.31219, 39.06925, 285.48868
48generate(-0.458786, 0.030183, 0.887963), (0.445214, 0.872709, 0.200375), (-0.768968, 0.487356, -0.413924)25.66225, -69.08205, 258.07117
49generate(0.566112, 0.680314, 0.465501), (0.680341, -0.704463, 0.202219), (0.465479, 0.202201, -0.861649)-18.53602, -92.05494, 196.89532
50generate(0.599491, -0.60298, 0.526371), (-0.713955, -0.105636, 0.692088), (-0.361816, -0.790759, -0.493855)-29.67262, -20.90009, 229.09175
51generate(0.672306, 0.504908, 0.541355), (-0.292656, -0.490405, 0.82082), (0.679956, -0.710415, -0.181901)-38.6598, -78.36067, 87.83308
52generate(-0.314291, 0.188684, 0.930315), (0.917722, -0.190364, 0.348668), (0.242926, 0.963464, -0.113385)6.18851, -134.03554, 121.18442
53generate(-0.996944, 0.064956, 0.043433), (0.064985, 0.379848, 0.922702), (0.043458, 0.922836, -0.382905)187.43134, -126.17777, 175.49107
54generate(0.387594, 0.763203, -0.51697), (0.709653, 0.110929, 0.695754), (0.588384, -0.63667, -0.498523)126.38496, -159.01826, 137.82809
55generate(0.286498, -0.877269, -0.385113), (0.180162, -0.345538, 0.920907), (-0.941059, -0.333202, 0.05904)119.02617, -137.08047, 213.25359
56generate(-0.931528, -0.099465, 0.349726), (-0.099488, -0.855479, -0.508143), (0.349873, -0.508242, 0.787008)141.30719, 75.64644, -6.15155
57generate(-0.314344, 0.917719, 0.242887), (0.188751, -0.190363, 0.963351), (0.930429, 0.348644, -0.113334)95.5171, -143.42599, 54.70642
58generate(-0.314759, -0.781319, 0.538929), (0.837645, -0.495723, -0.229307), (0.446438, 0.379319, 0.810481)57.09, -51.19205, -18.53819
59generate(0.559495, 0.425804, 0.711084), (-0.8112, 0.457307, 0.364378), (-0.170042, -0.780825, 0.601238)-49.80698, 31.08419, 68.25518
60generate(-0.314793, 0.837666, 0.446314), (-0.781267, -0.495705, 0.379254), (0.539045, -0.22942, 0.810498)69.12751, 26.25719, -27.494

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Components

#1: Protein
Capsid protein / Core antigen / Core protein / HBcAg / p21.5


Mass: 16791.104 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis B virus subtype adyw / Strain: ADYW / Gene: C / Plasmid: PET11B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 DE3 GOLD / References: UniProt: P03147
#2: Chemical ChemComp-0YP / N-[(1E)-1-bromo-1-(2-methoxyphenyl)-3-oxo-3-(piperidin-1-yl)prop-1-en-2-yl]-4-nitrobenzamide


Mass: 488.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H22BrN3O5
Sequence detailsTHE CYSTEINES AT POSITION 150 OF ALL CHAINS ON THE DEPOSITED STRUCTURES WERE ADDITIONAL RESIDUES ...THE CYSTEINES AT POSITION 150 OF ALL CHAINS ON THE DEPOSITED STRUCTURES WERE ADDITIONAL RESIDUES APPENDED TO THE NATIVE SEQUENCE TO CREATE COVALENT CROSSLINKS IN THE CAPSID STRUCTURE AND IMPROVE DIFFRACTION OF CRYSTALLIZED CAPSIDS

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Experimental details

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Experiment

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

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Sample preparation

Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 5% PEG 5000, 5% PEG 8000, 9% 2,3-butanediol, 300mM KCl, 150mM NaCl, 100mM Tris-HCl, pH 9.0, vapor diffusion, sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 70 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 12, 2009 / Details: Bent conical Si-mirror (Rh coated)
RadiationMonochromator: Bent Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.886→40 Å / Num. obs: 443831 / % possible obs: 61.1 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.144 / Net I/σ(I): 10.9
Reflection shell
Resolution (Å)Redundancy (%)Diffraction-ID% possible allRmerge(I) obs
4.2-4.272.5135.8
4.27-4.352.5157.80.948
4.35-4.432.5157.40.816
4.43-4.522.5157.50.701
4.52-4.622.6157.30.577
4.62-4.732.6157.10.526
4.73-4.842.6157.30.446
4.84-4.972.6157.10.383
4.97-5.122.6156.80.391
5.12-5.282.6156.60.364
5.28-5.472.6156.70.324
5.47-5.692.6156.70.318
5.69-5.942.6156.60.302
5.94-6.252.6156.80.243
6.25-6.642.5157.90.218
6.64-7.142.5160.70.165
7.14-7.842.3167.60.121
7.84-8.922.2178.90.073
8.92-11.082.3186.30.049
11.08-252.4192.30.064

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 49.21
Highest resolutionLowest resolution
Rotation8 Å41.75 Å
Translation8 Å41.75 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.1.4phasing
CNSrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.2→40 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
Details: WHILE THERE WAS DATA EXTENDING TO ~3.9 ANGSTROMS AND THIS VALUE WAS USED IN THE COURSE OF SOLVING THE STRUCTURE, WE IMPOSED A DATA-CUTOFF OF 4.2 ANGSTROMS FOR REPORTING RESOLUTION, AS THIS ...Details: WHILE THERE WAS DATA EXTENDING TO ~3.9 ANGSTROMS AND THIS VALUE WAS USED IN THE COURSE OF SOLVING THE STRUCTURE, WE IMPOSED A DATA-CUTOFF OF 4.2 ANGSTROMS FOR REPORTING RESOLUTION, AS THIS WAS THE HIGHEST RESOLUTION AT WHICH I/SIGMA > 1
RfactorNum. reflection% reflection
Rfree0.3826 31611 3.5 %
Rwork0.3787 --
obs0.3787 -71.1 %
Solvent computationBsol: 3221.6599 Å2
Displacement parametersBiso mean: 88.2026 Å2
Refinement stepCycle: LAST / Resolution: 4.2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4482 0 62 0 4544
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d0.996
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.7551.5
X-RAY DIFFRACTIONc_mcangle_it3.2922
X-RAY DIFFRACTIONc_scbond_it1.3342
X-RAY DIFFRACTIONc_scangle_it2.472.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.89-4.020.478821790.5057423814456050
4.02-4.190.497130860.4911592256231169.9
4.19-4.380.483130920.4761602886338071
4.38-4.610.468231620.464601066326871
4.61-4.890.454331950.4442598936308870.7
4.89-5.270.434231680.4286597986296670.6
5.27-5.80.435630960.4314597056280170.3
5.8-6.640.453531270.4418596246275170.2
6.64-8.350.409532490.3989620786532773
8.35-400.266842570.2652805608481794.1
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param
X-RAY DIFFRACTION5CNS_TOPPAR:carbohydrate.param
X-RAY DIFFRACTION6AT0.par

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