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- PDB-3szo: IspH:HMBPP complex after 3 minutes X-ray pre-exposure -

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Basic information

Entry
Database: PDB / ID: 3szo
TitleIspH:HMBPP complex after 3 minutes X-ray pre-exposure
Components4-hydroxy-3-methylbut-2-enyl diphosphate reductase
KeywordsOXIDOREDUCTASE / 4Fe-4S iron-sulfur cluster / conserved cysteine / IPP and DMAPP production final step / non-mevalonate pathway / substrate HMBPP / alternate conformations
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
Chem-H6P / IRON/SULFUR CLUSTER / 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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_comp_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_comp_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_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_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)73,6746
Polymers72,4462
Non-polymers1,2274
Water10,863603
1
A: 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8373
Polymers36,2231
Non-polymers6142
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)36,8373
Polymers36,2231
Non-polymers6142
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.890, 80.580, 111.090
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: 36223.031 Da / Num. of mol.: 2
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-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#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.: 603 / 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: 2.19 Å3/Da / Density % sol: 43.83 %
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: 1.6→20 Å / Num. all: 84534 / Num. obs: 77603 / % possible obs: 91.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.5
Reflection shellResolution: 1.6→1.7 Å / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 3.2 / % possible all: 95.6

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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: 1.6→10 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.454 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23903 3865 5 %RANDOM
Rwork0.20501 ---
obs0.20673 73426 100 %-
all-77453 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.868 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å20 Å2
2---1.68 Å20 Å2
3---2.09 Å2
Refinement stepCycle: LAST / Resolution: 1.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4773 0 46 603 5422
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0224895
X-RAY DIFFRACTIONr_angle_refined_deg1.651.9766644
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6995617
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.69524.159226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.87715853
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0281544
X-RAY DIFFRACTIONr_chiral_restr2.0940.2764
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213666
X-RAY DIFFRACTIONr_mcbond_it1.8751.53073
X-RAY DIFFRACTIONr_mcangle_it2.55324961
X-RAY DIFFRACTIONr_scbond_it3.94331822
X-RAY DIFFRACTIONr_scangle_it5.2384.51659
X-RAY DIFFRACTIONr_rigid_bond_restr2.80734895
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2383 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.430.5
Amedium thermal2.12
Bmedium positional0.430.5
Bmedium thermal2.12
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 287 -
Rwork0.252 5442 -
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)
111.9057-6.6947-4.03484.04763.05183.5448-0.1397-0.06410.00720.15110.11450.0030.20670.18540.02520.11120.021-0.02170.1310.02350.1264-6.2473-8.8142-7.0609
21.94211.06390.73420.87550.50980.31970.0375-0.0947-0.1494-0.028-0.018-0.0245-0.0029-0.0161-0.01950.133-0.0018-0.00390.1521-0.00210.0988-29.5056-10.2147-10.5691
32.42441.29170.54422.22911.85081.70680.03040.2219-0.0446-0.113-0.10890.0387-0.1257-0.19360.07850.05180.0287-0.04810.1003-0.0490.1118-40.3447-12.6207-22.3205
42.21410.74390.9590.2590.33050.42450.02570.0139-0.1449-0.00550.0422-0.0663-0.01720.031-0.0680.14920.00280.010.1552-0.01640.0967-26.0349-9.9842-22.1733
58.9997-8.02683.205916.42031.85943.57770.57191.11680.2314-0.5091-0.6946-0.36380.17130.47290.12270.04970.04850.01590.2432-0.10.1874-37.4581-9.1976-27.8657
60.37130.08150.54874.37251.44081.21340.07390.01350.0201-0.201-0.19730.31580.0276-0.03070.12340.13140.0178-0.0280.1525-0.02280.1158-41.1003-3.7333-20.801
71.5406-0.40611.84914.15913.75416.7894-0.0518-0.0894-0.35720.0632-0.06250.7645-0.0206-0.13430.11420.04990.0052-0.01610.0652-0.07360.4389-48.1740.4763-22.3487
80.30140.26880.22351.00261.00561.02970.0326-0.05130.01190.0913-0.10420.08910.0805-0.05770.07160.12050.0048-0.00660.167-0.01810.1096-38.71390.1753-10.9888
91.4163-2.47331.274410.62812.01434.0603-0.02890.0437-0.12480.5427-0.18820.86990.30430.03060.21710.0396-0.01450.05820.095-0.10140.2795-43.947615.8277-9.5244
100.6568-1.03-0.40082.37950.47820.27920.01360.0090.0145-0.1448-0.00140.0910.01720.0097-0.01220.14890.0108-0.02550.13740.00070.0927-30.602511.8762-17.7336
111.09480.4201-0.21162.3180.29140.22750.00770.09190.0389-0.2692-0.04290.157-0.03910.02210.03530.08530.0224-0.05040.09210.0150.0847-34.176521.3718-16.5258
120.8112-0.1444-0.10691.49970.04810.01490.02790.00810.03330.0837-0.0236-0.09570.0017-0.0049-0.00430.1340.0098-0.01160.1387-0.00990.0944-23.42514.4614-9.7938
130.6663-0.23590.34443.9095-3.17262.61160.0559-0.10730.04330.0502-0.02160.0654-0.0190.0017-0.03430.11270.00580.02250.1164-0.02170.0755-29.399422.4058-4.5924
141.8522-0.75850.13770.5889-0.27190.1788-0.0255-0.07780.11030.00980.0038-0.06380.0018-0.0010.02170.14040.0065-0.01290.1582-0.01570.0901-19.27022.9204-5.4337
151.45060.70210.48890.65540.57240.654-0.02130.02070.0094-0.04980.0049-0.0808-0.0312-0.04520.01640.1135-0.00130.00790.12030.0050.1212-11.27160.4859-15.9271
162.06520.3046-0.3792.04770.19323.2125-0.0640.0767-0.0949-0.31080.1067-0.2260.12440.1913-0.04270.06360.01920.04130.0996-0.00330.1188-3.0391-8.4201-20.9227
171.5313-0.48140.36850.88130.17650.2075-0.0085-0.0341-0.02060.05270.01460.01180.0314-0.0128-0.00610.13540.0065-0.00390.11980.0060.1028-14.6578-11.9849-13.4162
182.51060.047-0.75230.10410.34011.45520.0017-0.0937-0.12230.0403-0.0134-0.01280.10430.00090.01180.12030.0222-0.00650.08460.03450.1074-8.2231-11.8523-7.3411
198.30691.58093.83080.38250.85311.9561-0.0046-0.2664-0.08210.0525-0.0350.0270.0805-0.11160.03960.1325-0.00330.00550.17110.00910.0717-32.087-7.2924-2.0389
2033.1464-13.828-32.166745.7128.26740.5534-0.33320.3914-0.38841.0121-1.58871.0971-1.0914-2.3231.92190.30710.2281-0.19710.6067-0.46480.3589-44.5084-13.5169-8.4707
217.37155.0998-4.49614.5217-3.3943.6135-0.29730.2454-0.1313-0.31610.16180.08720.2297-0.07470.13550.0893-0.0191-0.02250.1246-0.02140.137-59.5145-8.83287.2291
220.6567-0.16680.1640.6238-0.25480.13470.00610.0066-0.02990.021-0.0149-0.01320.0343-0.01160.00880.14420.0025-0.0020.13260.00570.0868-34.6677-11.021517.7479
2316.82132.17576.622112.29027.76226.58360.8106-0.2956-0.7041-0.4453-0.2887-0.5572-0.0236-0.3084-0.52190.1710.0557-0.03710.25740.0690.0697-33.914-18.113225.5617
240.347-0.18730.18530.4614-0.42970.40140.0210.00580.0004-0.0103-0.00730.01360.0190.0022-0.01370.12920.0035-0.02180.1252-0.00320.0992-24.6686-5.648224.8915
250.1949-0.46120.07463.3314-2.47962.413-0.0380.07870.10640.0731-0.1734-0.36570.04180.04590.21140.0552-0.0105-0.02590.13040.03320.1758-18.77212.596820.5458
260.6271-0.2520.59690.5448-0.1711.1229-0.01070.10410.017-0.0982-0.0291-0.11870.07990.00870.03980.12220.0078-0.00130.13420.00860.1043-23.6722-3.837314.9283
271.09530.20750.20955.4491.60620.49510.10010.23040.0591-0.2952-0.02-0.3139-0.06240.0181-0.08010.094-0.01270.02070.14730.05130.1489-23.971912.39258.9066
280.92310.1119-0.291.0960.00730.09620.0088-0.04950.12190.16340.0134-0.06230.01570.0072-0.02220.1427-0.0113-0.02230.109-0.00330.1266-33.505813.326416.7168
291.32920.77080.76743.6811-0.06470.6115-0.0829-0.17140.2008-0.005-0.0461-0.38750.1132-0.11860.1290.2768-0.0013-0.09540.06630.00050.1811-24.196115.246818.0532
300.62530.03980.00331.1248-0.11010.02590.02720.03190.00970.0769-0.0114-0.03580.0174-0.03-0.01580.1254-0.00890.00570.11410.01690.0987-38.578519.749513.1928
311.8302-0.21680.17862.73622.37742.1417-0.00140.06230.1029-0.01970.0615-0.0832-0.00480.0691-0.06010.10610.00620.01140.09930.02970.0777-36.676822.77865.0229
320.48830.66060.05141.24310.50070.5443-0.01990.06210.0530.02730.05350.02550.0655-0.0096-0.03360.1432-0.0070.00320.14940.02070.0948-44.33443.22965.4969
335.6459-0.6776-0.31811.8888-0.8892.79810.21550.24060.0921-0.2157-0.10290.5341-0.09770.1026-0.11250.09450.0043-0.03910.1032-0.01810.1943-60.80670.13627.6663
342.3723-0.64480.90780.3339-0.67411.5311-0.05360.00670.03510.07410.0096-0.0053-0.13460.03080.0440.15280.01080.02490.12490.00610.0969-49.46050.232717.668
351.1464-1.73080.31094.0811-1.23920.53050.0075-0.04310.03370.17020.00560.1082-0.04590.0305-0.01310.1161-0.00730.03870.11410.00010.1294-57.0453-0.754118.4276
365.8993-1.8652.761.7596-0.22227.2177-0.1645-0.4382-0.18570.21920.03720.3571-0.0369-0.43160.12730.0707-0.02620.07640.10460.00530.134-64.0923-8.495320.9856
372.55520.46850.29391.13480.5510.50880.06640.0754-0.1350.0578-0.0332-0.02570.07120.0281-0.03310.1218-0.01370.0010.10730.00890.1121-51.2943-11.835813.5617
385.54432.7803-4.63684.3368-4.4126.4549-0.15830.3739-0.3052-0.14610.07620.10670.2694-0.17680.08210.0562-0.04540.00010.1045-0.0590.1108-58.221-11.92257.6224
396.8583-2.29334.1610.8042-1.43162.56910.01070.27060.0411-0.0821-0.0547-0.02310.0950.14210.04390.20280.00520.0180.2016-0.01560.0535-33.4296-7.91442.7999
4023.03187.84650.148452.97356.759533.1129-0.13571.41140.3389-0.6179-0.2466-1.82971.72240.60960.38230.19720.12140.0690.18820.07480.0948-22.8733-15.78617.7173
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 7
2X-RAY DIFFRACTION2A8 - 24
3X-RAY DIFFRACTION3A25 - 37
4X-RAY DIFFRACTION4A38 - 49
5X-RAY DIFFRACTION5A50 - 64
6X-RAY DIFFRACTION6A65 - 77
7X-RAY DIFFRACTION7A78 - 89
8X-RAY DIFFRACTION8A90 - 103
9X-RAY DIFFRACTION9A104 - 114
10X-RAY DIFFRACTION10A115 - 127
11X-RAY DIFFRACTION11A128 - 162
12X-RAY DIFFRACTION12A163 - 181
13X-RAY DIFFRACTION13A182 - 193
14X-RAY DIFFRACTION14A194 - 210
15X-RAY DIFFRACTION15A211 - 246
16X-RAY DIFFRACTION16A247 - 261
17X-RAY DIFFRACTION17A262 - 280
18X-RAY DIFFRACTION18A281 - 297
19X-RAY DIFFRACTION19A298 - 304
20X-RAY DIFFRACTION20A305 - 309
21X-RAY DIFFRACTION21B1 - 7
22X-RAY DIFFRACTION22B8 - 49
23X-RAY DIFFRACTION23B50 - 54
24X-RAY DIFFRACTION24B55 - 76
25X-RAY DIFFRACTION25B77 - 86
26X-RAY DIFFRACTION26B87 - 100
27X-RAY DIFFRACTION27B101 - 112
28X-RAY DIFFRACTION28B113 - 127
29X-RAY DIFFRACTION29B128 - 140
30X-RAY DIFFRACTION30B141 - 181
31X-RAY DIFFRACTION31B182 - 193
32X-RAY DIFFRACTION32B194 - 207
33X-RAY DIFFRACTION33B208 - 216
34X-RAY DIFFRACTION34B217 - 235
35X-RAY DIFFRACTION35B236 - 248
36X-RAY DIFFRACTION36B249 - 261
37X-RAY DIFFRACTION37B262 - 280
38X-RAY DIFFRACTION38B281 - 297
39X-RAY DIFFRACTION39B298 - 305
40X-RAY DIFFRACTION40B306 - 310

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