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- PDB-4h4c: IspH in complex with (E)-4-fluoro-3-methylbut-2-enyl diphosphate -

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Open data


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Basic information

Entry
Database: PDB / ID: 4h4c
TitleIspH in complex with (E)-4-fluoro-3-methylbut-2-enyl diphosphate
Components4-hydroxy-3-methylbut-2-enyl diphosphate reductase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / iron-sulfur protein / reductase / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
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-10D / 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: 1.8 Å
AuthorsSpan, I. / Eisenreich, W. / Jauch, J. / Bacher, A. / Groll, M.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2013
Title: Structures of Fluoro, Amino, and Thiol Inhibitors Bound to the [Fe(4) S(4) ] Protein IspH.
Authors: Span, I. / Wang, K. / Wang, W. / Jauch, J. / Eisenreich, W. / Bacher, A. / Oldfield, E. / Groll, M.
History
DepositionSep 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references
Revision 1.2Feb 20, 2013Group: Database references
Revision 1.3Sep 20, 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)72,5826
Polymers71,3512
Non-polymers1,2314
Water10,773598
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A: 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2913
Polymers35,6751
Non-polymers6162
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)36,2913
Polymers35,6751
Non-polymers6162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.360, 80.370, 111.070
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: 9 - 317

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

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999678, 0.010838, 0.022928), (0.010982, 0.999921, 0.006174), (-0.022859, 0.006424, -0.999718)-65.92735, 0.41788, -0.7151

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Components

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


Mass: 35675.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b0029, ispH, JW0027, lytB, yaaE / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-blue
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-10D / (2E)-4-fluoro-3-methylbut-2-en-1-yl trihydrogen diphosphate


Mass: 264.083 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11FO7P2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 598 / 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: 2.2 Å3/Da / Density % sol: 44.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Bis-Tris, 0.2 M ammonium sulfate, 25% PEG3350, pH 6.5, VAPOR DIFFUSION, SITTING 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: May 13, 2012
RadiationMonochromator: double-crystal fixed-exit Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→10 Å / Num. all: 59103 / Num. obs: 57685 / % possible obs: 97.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rsym value: 0.071 / Net I/σ(I): 10.8
Reflection shellResolution: 1.8→1.9 Å / Mean I/σ(I) obs: 2.3 / Rsym value: 0.489 / % possible all: 96.8

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Processing

Software
NameVersionClassification
XDSdata scaling
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
REFMAC5.6.0117phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KE8

3ke8


Resolution: 1.8→10 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.613 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.23224 2885 5 %RANDOM
Rwork0.18194 ---
obs0.1844 54799 97.65 %-
all-57684 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.538 Å2
Baniso -1Baniso -2Baniso -3
1-2.35 Å20 Å20 Å2
2---2.21 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4773 0 46 598 5417
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0194897
X-RAY DIFFRACTIONr_angle_refined_deg2.461.9776648
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1395617
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.81224.159226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.27815853
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8791544
X-RAY DIFFRACTIONr_chiral_restr0.1920.2764
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0213674
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2391 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.380.5
MEDIUM THERMAL2.492
LS refinement shellResolution: 1.8→1.845 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 194 -
Rwork0.254 3589 -
obs--96.04 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5982-0.27560.18350.59790.26580.3356-0.0696-0.0809-0.11980.15350.09680.01460.05850.0166-0.02720.04490.0206-0.01540.040.01170.1042-9.1944-7.925-7.2825
21.06110.31840.50550.30280.10250.25260.0959-0.097-0.0871-0.0448-0.0657-0.06610.0621-0.0373-0.03020.04090.0047-0.0040.0593-0.00420.0402-29.7576-10.1363-10.9128
31.7951-0.36880.58130.1249-0.08310.21960.10780.0769-0.1027-0.0268-0.06240.02850.039-0.004-0.04540.03580.0099-0.03260.0558-0.02730.0631-40.0461-13.2263-21.8823
41.35130.04210.0620.86420.26650.33740.03330.0005-0.0609-0.08850.02380.0248-0.00940.0158-0.05710.03870.0109-0.00240.0438-0.00970.0366-26.6117-10.154-21.5593
52.1221-1.18280.93042.02080.10710.69610.02530.2307-0.009-0.0892-0.05080.0611-0.02580.13060.02550.03240.0068-0.02970.0788-0.01410.029-37.1867-9.3009-27.6186
60.54420.36010.76171.0860.76771.14880.0596-0.04010.01060.0117-0.09540.05960.0695-0.08150.03570.02460.0117-0.01660.0639-0.01950.0485-40.9453-4.5955-20.7559
71.19941.49310.7482.7210.50050.6819-0.0658-0.04790.1116-0.12760.04980.2502-0.0196-0.08090.0160.01940.0137-0.04270.0647-0.01980.098-48.2766-0.0279-22.7607
80.12560.19450.29320.61510.2780.78970.01970.01570.00680.11960.01640.10720.00060.0213-0.03610.04420.00540.00620.0585-0.02120.0626-38.9069-0.4658-11.8714
91.4027-2.35390.71324.6348-0.38771.51040.0080.0163-0.13620.167-0.07580.4640.1771-0.02180.06790.0518-0.01260.08320.0324-0.04630.2031-43.736615.3903-9.1735
100.0570.025-0.01820.0172-0.01310.01010.00350.03750.063-0.02290.01780.0320.0186-0.013-0.02140.09410.0127-0.02240.05890.01650.0908-30.897612.0362-17.3478
110.64220.2828-0.15161.34080.15120.48320.03490.0480.0696-0.187-0.06440.1544-0.107-0.02450.02940.0530.0266-0.02780.0269-0.00480.0432-34.40720.975-16.3064
120.5131-0.11950.21351.3951-0.09380.4533-0.03150.0252-0.02280.087-0.0063-0.0104-0.040.0340.03780.03470.0082-0.00130.0362-0.00880.0271-24.116214.3629-10.0003
130.8682-0.27360.14653.3456-1.81370.98440.0821-0.02420.11630.1593-0.0590.0516-0.08320.0401-0.02310.07660.01330.00030.0435-0.00710.0357-29.322722.7721-5.3587
140.1413-0.2858-0.10820.64790.15460.1881-0.0008-0.01780.0090.01260.0130.00080.03550.0093-0.01220.0517-0.01420.00440.0488-0.00860.0376-19.41332.9061-5.6042
150.53880.1352-0.02330.35180.21920.1649-0.01710.0074-0.0151-0.04480.0291-0.0423-0.03020.0094-0.0120.02430.00720.00750.045-0.00250.0679-11.50220.4139-15.5058
161.41660.00260.3820.787-0.18832.3862-0.1810.0156-0.1116-0.21170.0522-0.20770.10850.18110.12880.0863-0.00240.06860.0345-0.02670.0982-2.5975-8.5075-20.2403
170.56010.34280.12510.21270.05750.3365-0.0002-0.0044-0.0520.00050.0019-0.04070.0569-0.0425-0.00180.03320.0059-0.00470.0288-0.00330.0585-14.766-11.6322-13.3646
181.2372-0.1216-1.02510.69190.67881.39670.0238-0.0424-0.12140.11520.0069-0.14460.1051-0.0178-0.03070.0451-0.0081-0.01710.0680.01660.0581-7.7121-11.8414-7.3794
194.3257-0.03872.79880.13590.32752.7311-0.1215-0.2723-0.05340.0338-0.00780.06060.0067-0.20610.12930.03390.00280.00780.047-0.00420.0474-31.7607-7.4808-2.1839
203.1379-1.3235-0.69776.15053.65695.3465-0.0265-0.1547-0.08140.2318-0.26420.36230.24-0.33680.29080.0421-0.05770.02270.0938-0.01890.0579-43.9161-13.7409-8.1489
210.15430.01480.12490.3019-0.00080.1103-0.0059-0.0473-0.0442-0.11080.01440.02-0.0036-0.0334-0.00860.0428-0.0136-0.00620.06640.00590.1051-56.5417-7.81067.7836
220.6539-0.17850.16220.2854-0.22610.19680.03060.0199-0.02290.0227-0.01260.01990.01570.0114-0.0180.0671-0.0007-0.00010.03460.00130.0328-33.7174-11.207617.7394
235.95390.8101-0.1650.17280.51614.66160.27090.0458-0.23560.04670.0157-0.06620.06630.0058-0.28670.05710.0074-0.02150.04840.0080.0319-33.7741-17.927225.2797
240.35950.18280.42231.1062-0.0780.58180.03630.014900.0605-0.0437-0.04650.03350.02930.00750.0327-0.0074-0.02160.05060.00270.0362-24.9553-5.961924.7885
250.2073-0.7143-0.21633.8338-1.20152.9906-0.01530.06550.02980.224-0.2988-0.3452-0.21720.04530.3140.0381-0.0247-0.06180.04240.03080.1098-18.42682.133820.7547
260.0948-0.22040.30780.6025-0.71641.01370.02940.02140.0146-0.1162-0.0558-0.11870.11920.0510.02640.05130.00470.01860.05720.01910.1123-23.3451-4.168615.7162
271.2595-0.7917-0.52964.91881.61460.59470.16780.13470.1954-0.233-0.0022-0.4123-0.1039-0.0378-0.16560.0442-0.01150.02260.05470.03640.0967-23.678612.18448.8879
280.26630.2392-0.4471.8974-0.81570.8563-0.04120.00430.05820.19340.0968-0.14560.0023-0.0227-0.05560.0569-0.0073-0.02640.0368-0.00510.0579-33.068713.287516.6872
291.2090.8846-0.83221.168-0.33470.7210.0016-0.1772-0.02380.027-0.0314-0.03340.01520.16880.02980.0546-0.0196-0.0480.05840.00630.1239-23.761514.967517.8048
300.64010.18370.08551.515-0.15140.29460.02460.00140.02440.0737-0.0146-0.0058-0.0584-0.0057-0.010.0454-0.01120.01540.01770.00320.0317-37.587319.808113.3606
311.3758-0.05520.54911.86291.65711.73450.0710.03140.1448-0.1154-0.0774-0.0649-0.0721-0.0590.00650.0828-0.00240.01720.01760.01930.0358-36.15122.82745.3613
320.0180.06560.00810.99790.43630.22320.00580.02520.01050.05580.0189-0.0210.0299-0.0282-0.02460.04370.0024-0.00130.04950.01370.0418-44.17323.23745.963
338.23961.2407-3.94712.8085-4.07336.60170.17880.15360.103-0.1312-0.00380.19490.0932-0.0582-0.17490.04230.0097-0.0350.0163-0.02680.15-60.45970.19917.8243
341.1421-0.0277-0.11060.5135-0.51950.54740.02840.05410.02190.0923-0.0140.0291-0.08770.0193-0.01430.05340.00390.03210.03890.00710.0607-49.28010.389117.2526
350.4788-0.76640.18271.3541-0.04640.7161-0.030.0128-0.01010.0881-0.0320.08490.0015-0.00710.0620.0363-0.00820.04660.03490.00390.0718-56.5783-0.438218.0684
362.0997-1.44521.8831.015-1.40155.494-0.1322-0.03950.01720.09880.02830.03120.3008-0.39560.1040.0779-0.04490.06280.0476-0.0220.1269-64.0264-8.174820.8767
370.0803-0.14760.06490.38280.01140.2070.00660.0171-0.02450.0275-0.00140.06270.04270.0508-0.00520.0367-0.00870.01620.03170.00480.0685-50.9706-11.474413.7185
382.46021.2635-2.17731.9659-2.3163.51550.01630.1933-0.0834-0.02920.07540.2020.0914-0.1106-0.09170.0215-0.00720.01160.0398-0.02250.0667-57.9901-11.68847.8356
392.3213-1.37651.48820.8689-1.01861.3832-0.09890.1075-0.03190.0274-0.0392-0.02730.04520.10030.1380.03980.01310.03530.11140.01560.0645-33.1109-7.84723.028
4019.84489.1293-5.625911.9387.815215.5979-0.60320.8942-0.6464-0.00660.4418-0.35650.5816-0.16240.16140.15330.11290.17350.19470.14360.2154-22.6779-15.81367.9109
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 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 DIFFRACTION21B2 - 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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