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- PDB-7lxr: Kinesin-like protein at 61F (Klp61f) bound to AMPPNP -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 7lxr
TitleKinesin-like protein at 61F (Klp61f) bound to AMPPNP
ComponentsKinesin-like protein Klp61F
KeywordsCELL CYCLE / microtubule-binding ATP-binding cell division mitosis plus-end directed motor protein
Function / homology
Function and homology information


aster / plus-end directed microtubule sliding / fusome organization / fusome / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / centrosome separation / spindle elongation / mitotic spindle microtubule / positive regulation of Golgi to plasma membrane protein transport ...aster / plus-end directed microtubule sliding / fusome organization / fusome / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / centrosome separation / spindle elongation / mitotic spindle microtubule / positive regulation of Golgi to plasma membrane protein transport / microtubule bundle formation / plus-end-directed microtubule motor activity / mitotic centrosome separation / microtubule associated complex / kinesin complex / microtubule-based movement / mitotic spindle pole / Golgi organization / cytoskeletal motor activity / protein secretion / mitotic spindle assembly / mitotic spindle organization / spindle microtubule / mitotic spindle / spindle / mitotic cell cycle / microtubule binding / microtubule / cell division / Golgi apparatus / endoplasmic reticulum / ATP binding / nucleus / cytoplasm
Similarity search - Function
Kinesin-associated microtubule-binding domain / Kinesin-associated microtubule-binding / : / : / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain ...Kinesin-associated microtubule-binding domain / Kinesin-associated microtubule-binding / : / : / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / IODIDE ION / Kinesin-like protein Klp61F
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.744 Å
AuthorsWorthylake, D.K. / Wojcik, E.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM097350 United States
Citation
Journal: To Be Published
Title: Crystal Structure of the Klp61f motor domain bound to AMPPNP
Authors: Wojcik, E.J. / Worthylake, D.K.
#1: Journal: J. Biol. Chem. / Year: 2010
Title: ATP hydrolysis in Eg5 kinesin involves a catalytic two-water mechanism
Authors: Parke, C.L. / Wojcik, E.J. / Kim, S. / Worthylake, D.K.
History
DepositionMar 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 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: Kinesin-like protein Klp61F
B: Kinesin-like protein Klp61F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,41512
Polymers82,8522
Non-polymers1,56310
Water5,927329
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A: Kinesin-like protein Klp61F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3347
Polymers41,4261
Non-polymers9086
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Kinesin-like protein Klp61F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0815
Polymers41,4261
Non-polymers6554
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.692, 50.813, 93.344
Angle α, β, γ (deg.)78.532, 77.869, 73.197
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Kinesin-like protein Klp61F / Bipolar kinesin KRP-130


Mass: 41425.965 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Klp61F, KLP2, CG9191 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): BL21 Star (DE3) / References: UniProt: P46863

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Non-polymers , 5 types, 339 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 329 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.75 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10% ethylene glycol, 50mM 4-(2-Hydroxyethyl)piperazine-1-ethanesulfonic acid sodium salt (sodium HEPES) pH 7.5, 180mM NaI and 15-17% polyethylene glycol MW 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Dec 29, 2012 / Details: Helios
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.74→48.11 Å / Num. obs: 67986 / % possible obs: 91.8 % / Redundancy: 3.31 % / Rmerge(I) obs: 0.0569 / Net I/σ(I): 12.56
Reflection shellResolution: 1.74→1.84 Å / Rmerge(I) obs: 0.2722 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 9356

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
SAINTdata reduction
SAINTdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HQD
Resolution: 1.744→48.11 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.937 / SU B: 5.203 / SU ML: 0.088 / Cross valid method: FREE R-VALUE / ESU R: 0.129 / ESU R Free: 0.124
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2238 2669 3.981 %
Rwork0.185 64375 -
all0.187 --
obs-67044 90.616 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 29.723 Å2
Baniso -1Baniso -2Baniso -3
1--0.593 Å20.341 Å20.235 Å2
2--0.678 Å2-0.956 Å2
3----0.119 Å2
Refinement stepCycle: LAST / Resolution: 1.744→48.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5431 0 82 329 5842
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0135663
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175503
X-RAY DIFFRACTIONr_angle_refined_deg1.9531.6567681
X-RAY DIFFRACTIONr_angle_other_deg1.4571.58312706
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6985712
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.0521.667300
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.326151072
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.631549
X-RAY DIFFRACTIONr_chiral_restr0.0960.2784
X-RAY DIFFRACTIONr_chiral_restr_other0.080.22
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026272
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021228
X-RAY DIFFRACTIONr_nbd_refined0.2340.21081
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2070.25382
X-RAY DIFFRACTIONr_nbtor_refined0.1640.22685
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.22927
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.2313
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1790.26
X-RAY DIFFRACTIONr_metal_ion_refined0.0910.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2710.222
X-RAY DIFFRACTIONr_nbd_other0.2570.296
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3280.220
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.3710.22
X-RAY DIFFRACTIONr_mcbond_it1.8332.0292773
X-RAY DIFFRACTIONr_mcbond_other1.8332.0292772
X-RAY DIFFRACTIONr_mcangle_it3.0823.0233468
X-RAY DIFFRACTIONr_mcangle_other3.0813.0243469
X-RAY DIFFRACTIONr_scbond_it2.3112.3722890
X-RAY DIFFRACTIONr_scbond_other2.312.3732891
X-RAY DIFFRACTIONr_scangle_it3.7553.4244199
X-RAY DIFFRACTIONr_scangle_other3.7543.4244200
X-RAY DIFFRACTIONr_lrange_it6.50824.7226153
X-RAY DIFFRACTIONr_lrange_other6.50724.7216154
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.744-1.790.2881570.2723894X-RAY DIFFRACTION73.5476
1.79-1.8390.2751720.2514545X-RAY DIFFRACTION89.3371
1.839-1.8920.2961720.2264506X-RAY DIFFRACTION89.8924
1.892-1.950.2471700.2094409X-RAY DIFFRACTION90.1378
1.95-2.0140.2262020.1854191X-RAY DIFFRACTION90.5586
2.014-2.0850.2141680.1784114X-RAY DIFFRACTION90.4329
2.085-2.1640.1981620.1763982X-RAY DIFFRACTION90.8971
2.164-2.2520.2041610.163845X-RAY DIFFRACTION90.9008
2.252-2.3520.231500.1733663X-RAY DIFFRACTION91.1111
2.352-2.4670.2021350.1783479X-RAY DIFFRACTION90.7812
2.467-2.60.2391430.1723344X-RAY DIFFRACTION91.2111
2.6-2.7580.2311420.1743142X-RAY DIFFRACTION90.8186
2.758-2.9480.2361320.1783029X-RAY DIFFRACTION92.1037
2.948-3.1840.2291300.1822806X-RAY DIFFRACTION93.772
3.184-3.4870.2231090.1892711X-RAY DIFFRACTION96.6415
3.487-3.8980.2091080.1762504X-RAY DIFFRACTION98.715
3.898-4.4990.2880.1632196X-RAY DIFFRACTION99.4773
4.499-5.5070.199840.1711868X-RAY DIFFRACTION99.2374
5.507-7.7740.331500.2271432X-RAY DIFFRACTION98.1457
7.774-48.110.17340.212715X-RAY DIFFRACTION89.2729
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.1785-0.2721-0.69680.66650.54280.91030.03140.0492-0.1442-0.1644-0.09520.1214-0.1198-0.07770.06370.0770.00890.00240.0796-0.00580.0877-3.0354-2.0207-10.1162
21.7109-1.5546-1.3831.59311.27721.12280.01410.02590.0789-0.04910.0494-0.1078-0.0191-0.0058-0.06340.0774-0.01260.03360.0951-0.0360.070711.8829-9.799-22.6826
30.5797-0.24070.66924.83361.30881.3327-0.03810.1184-0.0021-0.0948-0.0590.1517-0.10760.06990.09710.07520.0194-0.00220.1616-0.05760.0869-6.1296-4.2427-21.0566
40.49260.14470.01030.44520.62850.97440.01430.12430.0172-0.0801-0.05380.0274-0.1377-0.12570.03950.09150.0168-0.00880.08110.00350.0801-3.4489-1.4703-16.398
50.1548-0.1255-0.17580.63570.27070.23830.00170.0521-0.0035-0.0262-0.03180.0405-0.0149-0.04140.03010.07870.005-0.00050.07290.00140.108-0.35322.5063-1.1839
62.7966-0.17980.6492.56120.04062.68180.053-0.12860.3024-0.37460.1071-0.2877-0.490.3216-0.16010.15-0.08390.08840.0741-0.01610.17149.762215.7179-6.3296
70.5361-0.6406-0.5461.44880.82520.6012-0.01430.00640.07630.00150.0642-0.03690.01850.0104-0.04990.0903-0.00310.00680.03360.00780.13971.028517.08652.3743
80.3371-0.2057-0.24391.07930.38720.2608-0.0284-0.07130.00720.1593-0.013-0.04910.05110.03540.04150.10360.0121-0.02270.06720.00550.11418.48261.322112.0618
95.3354-1.3361.38980.3512-0.52892.9333-0.5799-0.5578-0.55610.12450.16670.1032-0.0332-0.07770.41320.1302-0.01090.07810.16020.0840.17557.1204-5.344520.6441
100.7718-6.1813-0.419449.60733.35950.22790.30980.0135-0.0283-2.3987-0.3350.2538-0.1623-0.00890.02520.16470.0059-0.07670.549-0.06580.0977-11.3014-2.2618.9066
118.56594.3943-3.52512.2595-1.80761.4527-0.00020.0580.2140.01340.06590.1204-0.0033-0.0169-0.06560.13330.063-0.0120.14680.06120.09071.9168-0.903618.1814
120.7102-0.3065-0.20971.96650.09670.33050.0152-0.12780.2172-0.00310.0462-0.23860.00280.0856-0.06140.0498-0.0029-0.02080.0623-0.0230.143611.935911.36958.0076
130.25020.0359-0.15820.14840.0920.3483-0.02440.0138-0.00210.0424-0.0209-0.03860.00560.04220.04540.0796-0.0045-0.00490.07630.01020.11699.04950.25433.0511
144.94153.63582.24874.8088-0.10276.9639-0.0730.0066-0.1110.0385-0.2774-0.05-0.2253-0.30040.35030.08510.01830.02030.1047-0.05430.0892-13.73521.919817.1988
151.1564-1.7861-1.42023.4172.44891.8436-0.0564-0.0152-0.08820.1355-0.0470.10640.0896-0.00830.10340.08670.00420.00440.067-0.00110.11020.03680.00224.2489
162.9616-0.15770.27760.04710.01070.06040.01670.0921-0.16130.0599-0.0078-0.01050.0634-0.0136-0.00890.1279-0.01540.01850.05090.00780.16067.0717-17.12062.2917
171.26810.45490.30060.76890.10810.47480.0071-0.0958-0.0530.1319-0.07240.08580.03390.01590.06540.0781-0.03450.03820.05750.02020.1242-7.8804-11.54437.4077
180.639-0.2515-0.54810.82690.70220.7975-0.01170.0439-0.028-0.0304-0.01060.0305-0.0188-0.0230.02230.07020.00340.00790.0824-0.01750.1009-0.936-7.2894-8.6256
192.9936-1.0752-1.70770.56760.98691.7599-0.04160.1103-0.07060.0584-0.04880.06180.1239-0.11360.09040.0582-0.01260.01850.0723-0.00910.153-9.2105-9.937-6.8518
201.61063.31732.4587.45356.58317.51920.1636-0.19670.07790.2055-0.39640.2137-0.0032-0.28220.23290.0993-0.03150.02490.0869-0.03840.125-14.8019.119813.9495
210.6640.79650.75051.83760.60860.99550.10760.2534-0.09210.0280.0115-0.07810.23160.3595-0.11910.10570.0603-0.01630.2056-0.07620.0828-2.2323-21.089836.9517
223.31011.46071.49540.97761.55923.13790.0099-0.2909-0.15380.0272-0.0818-0.03860.1222-0.11760.07190.1132-0.02830.00930.102-0.05180.0761-14.7536-31.233824.4452
230.2594-0.55310.65651.4947-0.21656.369-0.0086-0.01990.00230.00450.0813-0.05060.16010.0989-0.07280.09620.02420.01860.0837-0.06180.10083.008-29.013432.7819
240.84731.1341-0.10671.5305-0.15070.0210.0249-0.1107-0.05120.0006-0.0781-0.09390.0137-0.00950.05320.08810.01910.04290.2464-0.06380.1042.347-30.922416.6838
250.9447-0.9887-0.94261.08491.05871.0452-0.0331-0.07560.05190.1250.2036-0.15480.15780.2185-0.17060.13950.1166-0.11510.221-0.21660.21291.3029-25.948333.7063
260.16940.19040.1660.55090.28121.10630.04740.1073-0.09370.04290.041-0.12510.07690.0855-0.08840.07910.018-0.02720.1079-0.03740.069-5.7257-17.492945.8186
272.1450.1902-5.22322.7734-0.901712.8408-0.12520.10130.1263-0.16760.412-0.23150.4403-0.3667-0.28670.1518-0.0924-0.0260.18130.03920.0666-19.9008-23.955855.5044
284.94574.56575.83139.04228.73989.21410.12470.0553-0.16480.59520.0657-0.13340.50990.0829-0.19050.1856-0.0158-0.03270.02360.03770.0739-9.9024-27.336754.5169
290.58020.40450.19290.44790.21020.61120.0516-0.0423-0.02370.0533-0.0398-0.02980.0289-0.1953-0.01170.10870.0137-0.00780.0814-0.00630.023-12.7092-10.280753.2373
309.9603-0.0456-5.62471.6494-0.84153.6906-0.14050.31370.11230.01750.1369-0.0466-0.0339-0.25760.00360.19330.0221-0.06470.06510.02890.0803-18.86447.398344.78
3120.9701-5.10142.35775.6334-2.0170.73960.256-0.6072-0.3481-0.1379-0.2398-0.03160.05070.0548-0.01620.1417-0.0211-0.01030.0620.05710.14880.63377.984546.9747
320.63750.0583-0.11920.22330.3911.62920.04880.00210.04330.0748-0.05650.0656-0.0539-0.23680.00770.08980.01980.01280.0919-0.01550.0634-18.4229-7.149250.6475
330.6625-0.3829-0.20373.77342.68851.92940.04180.1491-0.0460.0193-0.26370.3132-0.0047-0.16750.22180.10140.0205-0.01410.1621-0.01690.0413-20.3954-15.103633.8033
340.47150.23380.35460.23960.48951.11710.0605-0.00030.04090.0280.0042-0.03150.09460.0057-0.06470.09910.005-0.00490.1219-0.01230.0802-3.8269-6.227457.3507
351.11540.0301-0.22950.0272-0.1241.1015-0.02680.09790.0995-0.02140.01070.0042-0.19440.07920.01610.1846-0.0353-0.01920.19160.04830.0179-11.0127-6.147727.3527
366.0653-0.323-2.71881.85771.39212.06410.1543-0.12760.4669-0.66530.2694-0.3081-0.52280.2468-0.42370.2429-0.13210.10090.22930.03750.12483.2432.264231.9453
374.1989-0.90331.81262.4469-0.30520.7891-0.13970.24240.0428-0.01860.13350.022-0.07880.12450.00620.142-0.05320.05010.16030.0430.0453-4.6088-0.961438.6939
380.06480.26820.30711.17451.04983.0514-0.02630.0017-0.008-0.08930.0323-0.05240.04110.1611-0.00610.06060.00980.00640.1379-0.05610.0653-3.8732-17.6831.5525
392.01691.18322.85061.87072.00324.1325-0.0810.2708-0.06170.01320.1851-0.0127-0.10220.4211-0.10410.0139-0.04390.0170.2147-0.04450.04866.0625-10.793136.251
400.71840.40741.18120.46351.77177.1997-0.04650.01550.059-0.04030.04640.0118-0.12490.14270.00010.0792-0.0154-0.0140.0971-0.00850.0864.8160.244561.101
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA18 - 29
2X-RAY DIFFRACTION2ALLA30 - 42
3X-RAY DIFFRACTION3ALLA43 - 53
4X-RAY DIFFRACTION4ALLA54 - 87
5X-RAY DIFFRACTION5ALLA88 - 115
6X-RAY DIFFRACTION6ALLA116 - 130
7X-RAY DIFFRACTION7ALLA131 - 151
8X-RAY DIFFRACTION8ALLA152 - 173
9X-RAY DIFFRACTION9ALLA174 - 182
10X-RAY DIFFRACTION10ALLA183 - 188
11X-RAY DIFFRACTION11ALLA189 - 196
12X-RAY DIFFRACTION12ALLA197 - 216
13X-RAY DIFFRACTION13ALLA217 - 242
14X-RAY DIFFRACTION14ALLA243 - 251
15X-RAY DIFFRACTION15ALLA252 - 268
16X-RAY DIFFRACTION16ALLA274 - 296
17X-RAY DIFFRACTION17ALLA297 - 323
18X-RAY DIFFRACTION18ALLA324 - 343
19X-RAY DIFFRACTION19ALLA344 - 358
20X-RAY DIFFRACTION20ALLA359 - 367
21X-RAY DIFFRACTION21ALLB18 - 29
22X-RAY DIFFRACTION22ALLB30 - 42
23X-RAY DIFFRACTION23ALLB43 - 52
24X-RAY DIFFRACTION24ALLB53 - 60
25X-RAY DIFFRACTION25ALLB61 - 74
26X-RAY DIFFRACTION26ALLB75 - 115
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