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- PDB-3szu: IspH:HMBPP complex structure of E126Q mutant -

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Open data


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Basic information

Entry
Database: PDB / ID: 3szu
TitleIspH:HMBPP complex structure of E126Q mutant
Components4-hydroxy-3-methylbut-2-enyl diphosphate reductase
KeywordsOXIDOREDUCTASE / 3Fe-4S iron-sulfur cluster / conserved cysteine / IPP and DMAPP production final step / non-mevalonate pathway / substrate HMBPP
Function / homology
Function and homology information


hydroxymethylbutenyl pyrophosphate reductase activity / 4-hydroxy-3-methylbut-2-en-1-yl diphosphate reductase / 4-hydroxy-3-methylbut-2-en-1-yl diphosphate reductase activity / dimethylallyl diphosphate biosynthetic process / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / 3 iron, 4 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / metal ion binding / cytosol
Similarity search - Function
4-hydroxy-3-methylbut-2-enyl diphosphate reductase / LytB protein / 4-hydroxy-3-methylbut-2-enyl diphosphate reductase, catalytic domain / Rossmann fold - #11270 / Cobalt-precorrin-4 Transmethylase; domain 1 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FE3-S4 CLUSTER / Chem-H6P / 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsSpan, I. / Graewert, T. / Bacher, A. / Eisenreich, W. / Groll, M.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Crystal Structures of Mutant IspH Proteins Reveal a Rotation of the Substrate's Hydroxymethyl Group during Catalysis.
Authors: Span, I. / Grawert, T. / Bacher, A. / Eisenreich, W. / Groll, M.
History
DepositionJul 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2012Group: Database references
Revision 1.2Feb 15, 2012Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
B: 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5606
Polymers72,4442
Non-polymers1,1164
Water9,530529
1
A: 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7803
Polymers36,2221
Non-polymers5582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7803
Polymers36,2221
Non-polymers5582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.190, 80.390, 112.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 4 / Auth seq-ID: 1 - 309 / Label seq-ID: 13 - 321

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein 4-hydroxy-3-methylbut-2-enyl diphosphate reductase / / IspH


Mass: 36222.047 Da / Num. of mol.: 2 / Mutation: E126Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ispH, lytB, yaaE, b0029, JW0027 / Production host: Escherichia coli (E. coli)
References: UniProt: P62623, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
#2: Chemical ChemComp-F3S / FE3-S4 CLUSTER / Iron–sulfur cluster


Mass: 295.795 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe3S4
#3: Chemical ChemComp-H6P / (2E)-4-hydroxy-3-methylbut-2-en-1-yl trihydrogen diphosphate / (E)-4-Hydroxy-3-methyl-but-2-enyl pyrophosphate


Mass: 262.092 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12O8P2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 529 / Source method: isolated from a natural source / Formula: H2O

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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: 2.18 Å3/Da / Density % sol: 43.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 200 mM lithium sulfate, 25% PEG3350, 100 mM Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 11, 2011
RadiationMonochromator: Fixed-exit LN2 cooled Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→20 Å / Num. all: 124650 / Num. obs: 124027 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 12.1
Reflection shellResolution: 1.4→1.5 Å / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 4.9 / % possible all: 99.9

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Processing

Software
NameClassification
XDSdata scaling
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3F7T
Resolution: 1.4→10 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.981 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21512 6233 5 %RANDOM
Rwork0.17476 ---
obs0.17676 118417 100 %-
all-124650 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.398 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å20 Å2
2---0.74 Å20 Å2
3---0.96 Å2
Refinement stepCycle: LAST / Resolution: 1.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4773 0 44 529 5346
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0224891
X-RAY DIFFRACTIONr_angle_refined_deg2.2571.9746630
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7145617
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.34624.159226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.47415853
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2421544
X-RAY DIFFRACTIONr_chiral_restr0.1950.2762
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0213674
X-RAY DIFFRACTIONr_mcbond_it2.3211.53075
X-RAY DIFFRACTIONr_mcangle_it3.11924965
X-RAY DIFFRACTIONr_scbond_it4.52731816
X-RAY DIFFRACTIONr_scangle_it6.4674.51653
X-RAY DIFFRACTIONr_rigid_bond_restr2.77234891
X-RAY DIFFRACTIONr_sphericity_free9.5773529
X-RAY DIFFRACTIONr_sphericity_bonded4.72534819
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2390 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.40.5
Amedium thermal1.782
Bmedium positional0.40.5
Bmedium thermal1.782
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 451 -
Rwork0.2 8562 -
obs--100 %
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)
11.1634-0.0742-0.15380.08370.00370.13630.0155-0.0902-0.10380.0396-0.01130.00020.03780.014-0.00430.0409-0.0014-0.01520.02820.00150.0162-8.9613-8.0386-6.8263
21.39810.17280.68980.4848-0.15750.46780.0946-0.082-0.1205-0.0331-0.0307-0.0090.0686-0.0272-0.06390.0237-0.0062-0.00490.0273-0.00720.0199-29.3587-10.1888-10.2953
31.8655-0.16211.31460.0359-0.07880.98420.25460.1988-0.1961-0.0258-0.07970.00070.18270.0537-0.1750.05890.0403-0.04120.15280.01530.0444-39.903-12.9632-21.9666
42.6998-0.61060.4520.50770.01180.1110.07210.0884-0.2137-0.0824-0.03620.0464-0.00970.0095-0.03590.02630.0086-0.00430.027-0.02050.0255-25.9595-10.0881-21.7496
52.9878-1.16031.07481.48860.15220.69970.00080.2959-0.0413-0.0194-0.0150.0605-0.01410.15720.01420.02080.0202-0.0210.0629-0.0220.0225-37.2214-10.0253-27.9274
60.46250.55580.61490.82260.79430.83740.01880.01180.0189-0.0122-0.06080.07450.0132-0.01150.0420.02040.0127-0.01140.0403-0.02160.0216-41.2034-4.0508-20.7483
70.97161.28170.37964.45082.23012.20440.0173-0.01070.1490.0455-0.150.45860.0001-0.15670.13270.02270.0225-0.02590.0344-0.04180.1049-48.3963-0.2456-22.0407
80.08-0.0377-0.05190.23520.29640.38090.0217-0.00830.02070.0268-0.03650.02190.0294-0.04090.01480.0209-0.00370.01460.0341-0.01140.0261-38.6687-0.1353-10.7818
90.8425-1.92370.68597.2055-1.12890.6511-0.075-0.0457-0.08740.47950.12890.6366-0.0219-0.0172-0.05390.04600.07780.0133-0.02280.1741-43.555315.9105-8.8622
100.3169-0.3922-0.1161.37730.17670.0516-0.00170.00470.0283-0.12740.01180.0761-0.01260.0081-0.01020.0406-0.0015-0.00870.0221-0.00040.02-30.425411.4428-17.9924
110.43430.05880.17591.0707-0.29920.3442-0.01820.09150.0551-0.03610.00530.1598-0.07310.01750.01290.03810.0067-0.02040.02230.00680.0386-34.177221.0136-16.3339
120.20090.07130.26181.0467-0.06120.3649-0.01590.0045-0.00120.04330.0057-0.0693-0.0280.00270.01020.02040.00010.00390.0152-0.00880.0126-23.425414.1471-9.9604
131.3023-0.53360.5290.7648-0.81660.87410.0416-0.02110.06420.07160.00160.0418-0.07660.0032-0.04320.0739-0.00090.02080.0035-0.00620.0182-29.290122.4303-4.7466
140.3873-0.4247-0.11610.5392-0.01140.3037-0.0117-0.02650.02880.02340.0195-0.0291-0.00950.0128-0.00780.0202-0.0080.00180.0299-0.0140.0088-19.21362.8068-5.192
150.50120.02920.0470.29230.13190.0720.02760.02010.0294-0.0276-0.0118-0.0688-0.0081-0.0187-0.01580.010.00080.01250.0245-0.01110.0334-11.32460.4541-15.8387
162.1015-0.3803-0.58930.1435-0.01721.96520.0140.1392-0.146-0.0501-0.0051-0.05290.02540.1442-0.00880.0321-0.01820.05540.0432-0.05470.1151-2.8822-8.6367-20.8706
170.40610.1864-0.08370.11950.02090.12130.0375-0.016-0.06740.03-0.0174-0.04970.0135-0.0141-0.020.0163-0.0002-0.00990.0190.00010.0313-14.5848-12.0539-13.3099
181.3476-0.2335-0.78660.77360.48290.8944-0.003-0.1529-0.13810.07950.0443-0.11630.0770.0709-0.04130.01980.0078-0.02330.03480.01660.0524-7.8846-11.6429-7.0909
191.71710.1280.85680.01160.1021.4158-0.0165-0.172-0.0978-0.0015-0.0084-0.00510.0563-0.08310.02490.0225-0.00870.00840.03440.00660.0116-31.313-7.3379-1.6819
201.71382.3084-1.910510.72274.48628.67770.0302-0.02260.04630.4164-0.36730.48040.3251-0.29890.33710.0321-0.04270.01850.0659-0.01320.0249-43.9833-13.5768-7.6827
211.7588-0.2249-0.110.1432-0.04710.252-0.0180.0943-0.2281-0.00920.00420.12940.0210.00090.01380.0179-0.0002-0.00060.00870.00560.1314-56.483-7.54087.7794
220.4795-0.1850.21520.5072-0.10140.21140.04380.0241-0.03640.06440.00830.03310.03940.0118-0.05210.03180.0029-0.00470.01310.00270.0174-33.9205-10.904818.093
236.78271.0597-2.59590.2266-0.55051.33880.1025-0.0441-0.1101-0.0064-0.02590.03170.02170.0582-0.07660.0619-0.0153-0.03610.0149-0.00750.0462-33.6596-17.775525.778
240.10560.16640.08790.28540.09590.16710.05120.0025-0.01860.0763-0.012-0.02160.04780.0238-0.03920.039-0.0023-0.01380.0273-0.00010.0145-24.3269-5.57725.1932
250.5432-0.30610.94733.1783-0.9631.7135-0.03790.06170.03020.0968-0.0552-0.3185-0.07430.10890.09310.0217-0.0102-0.03160.02360.01050.0601-18.17922.281621.0424
260.2725-0.33050.36460.4673-0.39670.57050.01390.0310.0086-0.02120.0174-0.0485-0.01350.0676-0.03130.01840.00060.00920.0538-0.02240.0329-23.3787-3.922715.3604
271.1657-1.0841-0.34484.06131.18290.3460.10060.05830.1859-0.30440.046-0.492-0.08740.008-0.14660.0344-0.01520.03860.02760.00840.0818-23.657312.11238.7474
280.4060.7713-0.21761.9805-0.68350.52140.0022-0.0180.02770.12120.0288-0.0561-0.0301-0.0044-0.0310.05310.0103-0.01870.0153-0.02260.0538-32.823413.2717.1793
290.44990.5727-0.28592.0241-0.06980.2520.0144-0.0783-0.00870.06890.0152-0.21150.00970.0723-0.02960.0192-0.0087-0.01150.031-0.0120.0699-23.235815.148317.9828
300.44370.08280.20021.15860.01370.1433-0.0207-0.00230.03670.06170.03540.0426-0.04530.0073-0.01470.03-0.00090.02310.0077-0.00010.0253-37.893719.773813.4124
310.9858-0.04780.01921.12120.69450.43270.03710.04770.0846-0.09630.0124-0.0896-0.05680.009-0.04950.06940.00140.02610.00260.00350.0182-36.145222.98765.4785
320.07370.20090.10620.6050.43520.5263-0.0150.01270.0236-0.03890.02310.0469-0.0133-0.0064-0.0080.01390.00510.00480.02090.01660.0251-44.02343.3525.9524
334.6519-1.1623-1.23570.5103-0.59294.07660.3310.103-0.1496-0.0818-0.07680.1319-0.08430.1557-0.25420.02830.00570.01760.0122-0.03140.2333-60.65810.46018.3141
340.5229-0.23310.00040.535-0.14880.05710.02080.0111-0.00220.12050.00770.126-0.04040.0067-0.02850.04170.00950.04520.02010.02210.06-49.09850.487517.7835
350.554-1.09040.0572.29250.23460.8517-0.04670.0267-0.07640.1143-0.06070.21420.012-0.03460.10730.03040.00820.05350.00790.0110.1024-56.5233-0.300418.599
364.464-2.7851.37612.078-2.39478.7581-0.66480.0067-0.08670.42070.12720.09290.1517-0.64890.53750.2013-0.0180.21170.0522-0.02190.3932-63.781-7.667721.6647
370.4655-0.2096-0.10491.4670.1220.02910.0170.0692-0.03890.1074-0.02680.2133-0.0006-0.01350.00980.0160.0010.02810.0207-0.00170.0815-50.8217-11.546114.0923
383.16840.8932-2.91886.109-4.23385.43610.08680.4893-0.4122-0.34720.07180.99410.1807-0.172-0.15860.02730.0289-0.07530.1497-0.04620.2775-57.81-11.16357.9209
391.3206-0.23720.89270.125-0.39831.3088-0.03790.1165-0.0623-0.0093-0.0046-0.01350.03580.05890.04250.01860.01080.01680.03780.0030.0178-33.304-7.80763.1484
405.62890.1207-0.84659.3547-0.57386.31870.11960.1394-0.0887-0.3587-0.3105-0.40310.37820.13460.19090.04780.03410.02030.03040.01140.0233-22.3908-15.73238.0694
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 7
2X-RAY DIFFRACTION1A997
3X-RAY DIFFRACTION2A8 - 24
4X-RAY DIFFRACTION3A25 - 37
5X-RAY DIFFRACTION4A38 - 49
6X-RAY DIFFRACTION5A50 - 64
7X-RAY DIFFRACTION6A65 - 77
8X-RAY DIFFRACTION7A78 - 89
9X-RAY DIFFRACTION8A90 - 103
10X-RAY DIFFRACTION9A104 - 114
11X-RAY DIFFRACTION10A115 - 127
12X-RAY DIFFRACTION11A128 - 162
13X-RAY DIFFRACTION12A163 - 181
14X-RAY DIFFRACTION13A182 - 193
15X-RAY DIFFRACTION14A194 - 210
16X-RAY DIFFRACTION15A211 - 246
17X-RAY DIFFRACTION16A247 - 261
18X-RAY DIFFRACTION17A262 - 280
19X-RAY DIFFRACTION18A281 - 297
20X-RAY DIFFRACTION19A298 - 304
21X-RAY DIFFRACTION20A305 - 309
22X-RAY DIFFRACTION21B1 - 7
23X-RAY DIFFRACTION21B997
24X-RAY DIFFRACTION22B8 - 49
25X-RAY DIFFRACTION23B50 - 54
26X-RAY DIFFRACTION24B55 - 76
27X-RAY DIFFRACTION25B77 - 86
28X-RAY DIFFRACTION26B87 - 100
29X-RAY DIFFRACTION27B101 - 112
30X-RAY DIFFRACTION28B113 - 127
31X-RAY DIFFRACTION29B128 - 140
32X-RAY DIFFRACTION30B141 - 181
33X-RAY DIFFRACTION31B182 - 193
34X-RAY DIFFRACTION32B194 - 207
35X-RAY DIFFRACTION33B208 - 216
36X-RAY DIFFRACTION34B217 - 235
37X-RAY DIFFRACTION35B236 - 248
38X-RAY DIFFRACTION36B249 - 261
39X-RAY DIFFRACTION37B262 - 280
40X-RAY DIFFRACTION38B281 - 297
41X-RAY DIFFRACTION39B298 - 305
42X-RAY DIFFRACTION40B306 - 310

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