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- PDB-4eb3: Crystal structure of IspH in complex with iso-HMBPP -

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Basic information

Entry
Database: PDB / ID: 4eb3
TitleCrystal structure of IspH in complex with iso-HMBPP
Components4-hydroxy-3-methylbut-2-enyl diphosphate reductase
KeywordsOXIDOREDUCTASE / iron-sulfur protein / reductase / (E)-4-hydroxy-3-methylbut-2-enyl diphosphate (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-enyl 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-0O3 / 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: 1.9 Å
AuthorsWang, W. / Wang, K. / Span, I. / Bacher, A. / Groll, M. / Oldfield, E.
CitationJournal: J.Am.Chem.Soc. / Year: 2012
Title: Are free radicals involved in IspH catalysis? An EPR and crystallographic investigation.
Authors: Wang, W. / Wang, K. / Span, I. / Jauch, J. / Bacher, A. / Groll, M. / Oldfield, E.
History
DepositionMar 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 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)73,4436
Polymers72,2162
Non-polymers1,2274
Water6,882382
1
A: 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7223
Polymers36,1081
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)36,7223
Polymers36,1081
Non-polymers6142
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.580, 80.820, 113.050
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

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999778, 0.009693, 0.018721), (0.009646, 0.99995, -0.002599), (-0.018745, -0.002418, -0.999821)-65.77703, 0.38502, -0.56827

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Components

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


Mass: 36107.941 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 / 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


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-0O3 / 3-(hydroxymethyl)but-3-en-1-yl trihydrogen diphosphate


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


Mass: 18.015 Da / Num. of mol.: 382 / 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: 2.23 Å3/Da / Density % sol: 44.9 %
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: Jan 27, 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: 1.9→15 Å / Num. all: 51491 / Num. obs: 51490 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2.02 / Rmerge(I) obs: 0.068 / Net I/σ(I): 11.6
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.5 / % possible all: 99.1

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Processing

Software
NameVersionClassification
RemDAqdata collection
REFMAC5refinement
XDSdata reduction
XSCALEdata scaling
REFMAC5phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KE8
Resolution: 1.9→15 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.954 / SU B: 5.952 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22824 2581 5 %RANDOM
Rwork0.18924 ---
obs0.19122 49037 99.89 %-
all-49091 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.532 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å20 Å2
2---1.94 Å20 Å2
3---2.29 Å2
Refinement stepCycle: LAST / Resolution: 1.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4773 0 46 382 5201
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0194897
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0741.9776648
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8345617
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.21324.159226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.78715853
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2991544
X-RAY DIFFRACTIONr_chiral_restr0.1580.2766
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213664
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.370.5
MEDIUM THERMAL2.212
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 172 -
Rwork0.233 3283 -
obs--99.74 %
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)
111.8806-7.8482-6.75825.47973.79545.4451-0.5095-0.36220.07220.38540.3304-0.16060.32140.11740.17910.1690.0925-0.10320.1658-0.01450.227-6.0211-8.9993-7.5756
22.12050.10690.97990.6396-0.14410.51460.0849-0.1382-0.1482-0.0987-0.0511-0.0550.0585-0.0459-0.03390.1811-0.0001-0.02920.1693-0.0160.1467-29.8434-10.1971-10.9949
32.79730.0380.52922.1517-0.14690.12010.36160.3398-0.18990.0305-0.3677-0.13640.06260.07240.00610.18950.0115-0.09770.1539-0.04850.1502-40.4017-13.413-21.807
46.0201-2.1735-0.28031.03410.0320.03250.19890.2284-0.31140.0196-0.22050.0586-0.03770.02790.02160.16780.0374-0.02420.1635-0.04320.1696-26.831-10.2671-21.6827
53.1381-0.69172.95710.3617-0.62352.80530.17710.7959-0.0979-0.0963-0.11030.00670.13590.7079-0.06690.14990.0737-0.08190.385-0.09310.0876-37.4724-9.6465-27.7512
60.87690.71880.78742.16851.25650.94580.05360.01870.1166-0.0371-0.16180.14470.0332-0.04770.10820.16530.0053-0.04680.202-0.03130.1303-41.2482-4.6983-20.9093
71.33640.08440.0443.5242.37162.8531-0.02270.12720.16170.0014-0.06850.5264-0.0565-0.0990.09120.10230.0305-0.06970.1481-0.04230.2315-48.6587-0.2621-22.9141
80.68220.5454-0.15960.4692-0.02040.53260.0792-0.04270.12190.0974-0.07930.12480.1489-0.00550.00010.15740.007-0.01460.1873-0.03770.1624-39.0734-0.539-11.9583
95.5436-1.5301-1.60527.3922-4.37093.7930.1651-0.06310.18830.32180.22830.5074-0.2765-0.1115-0.39330.10070.02150.12570.1083-0.05520.3784-43.801615.4539-8.9453
100.2966-0.765-0.36323.53040.85460.45230.0080.01540.0893-0.18320.12230.11370.0069-0.0067-0.13040.17220.0177-0.02680.1667-0.00030.1562-31.104812.0657-17.5396
111.43430.5236-0.31121.6690.03730.56240.08130.14910.0912-0.1848-0.04490.256-0.1586-0.003-0.03640.15250.0517-0.03230.12930.02360.1784-34.615621.0114-16.4587
120.09610.1873-0.05161.9011-0.89890.4510.04620.01790.01950.1164-0.0531-0.0247-0.00890.02030.00690.17780.00980.00320.163-0.01410.1396-24.090814.3882-10.3542
133.0087-0.23630.46234.8637-3.66452.7910.18460.05320.1520.1552-0.04770.236-0.08650.06-0.13680.23740.02190.0450.122-0.0250.1318-29.291622.8726-5.5804
141.5541-0.4683-0.64070.49160.0880.30120.0643-0.04120.07770.0609-0.0437-0.0567-0.02320.0208-0.02060.1888-0.0072-0.0330.1798-0.00850.1362-19.29182.9214-5.9591
151.07090.4815-0.12460.58770.33850.46360.03190.0607-0.0384-0.04190.0076-0.1236-0.0432-0.0585-0.03950.14970.0110.01330.1487-0.00770.2063-11.45920.4434-16.0424
163.70120.7709-0.66730.945-0.70512.6748-0.190.1486-0.1357-0.24840.1109-0.40610.22120.12340.07910.10720.01950.08710.1171-0.04440.2593-2.6017-8.4691-21.035
170.94910.4433-0.5050.7803-0.01950.35860.0533-0.0546-0.09290.0805-0.0652-0.14460.0036-0.01830.01190.17450.015-0.01990.1527-0.00380.1813-14.6841-11.6926-13.841
183.4068-0.4461-1.35231.51711.81952.6850.0336-0.2008-0.24840.29120.092-0.31510.35770.0572-0.12560.1320.055-0.03450.1230.00130.2324-7.4723-11.8089-7.9819
197.1110.87033.54110.10680.44052.5932-0.1276-0.1368-0.178-0.0172-0.0093-0.01950.0747-0.12350.13680.1917-0.0055-0.01720.18190.00360.1146-31.6444-7.3781-2.1959
208.5033-5.2748-5.9037.41813.441617.80760.2395-0.168-0.54960.692-0.59460.7372-0.4077-0.82650.35510.1833-0.12910.05080.2103-0.0470.1579-43.9059-13.5313-7.9587
2110.31888.2944-4.81067.0108-3.02154.3551-0.69530.25150.1248-0.67960.21780.34440.108-0.16290.47750.1174-0.0613-0.16410.12150.030.4472-59.6562-8.88138.1952
221.4249-0.59710.44190.7363-0.07980.180.07110.0331-0.07560.07030.00550.01050.0774-0.0061-0.07660.1832-0.0079-0.04330.14040.02080.148-33.3854-11.183917.8776
232.17680.46224.22710.4620.87338.21070.4206-0.1132-0.30820.53020.1358-0.17050.7045-0.2322-0.55640.64820.087-0.19650.13290.04650.1451-33.4429-17.934725.5198
240.56210.33810.45941.5999-0.5510.87940.0741-0.0023-0.02880.074-0.0257-0.03760.03820.0308-0.04840.16350.0016-0.05840.179-0.00420.1438-24.6187-5.903924.974
250.4708-1.6680.53076.3472-2.94693.2459-0.06440.04740.1510.195-0.1527-0.5513-0.13480.0310.21710.152-0.0303-0.08930.14370.01890.2216-18.09382.204821.0353
260.8762-0.85971.07010.8971-1.08311.45340.01360.02890.1276-0.0998-0.0494-0.1480.14440.00930.03580.17430.0144-0.03970.17280.00870.1775-22.9747-4.081215.8825
274.25641.1355-1.66847.15610.81160.88640.30160.15570.316-0.1931-0.0547-0.704-0.1464-0.0918-0.24690.1344-0.00130.03630.14250.03510.3223-23.441912.28238.7003
280.1941-0.1453-0.18823.1225-0.62630.3827-0.0214-0.00150.12250.22510.0956-0.3268-0.0286-0.0463-0.07420.1592-0.0202-0.02460.15160.0020.1896-32.832113.396216.721
291.97472.4328-0.5058.49411.42880.9235-0.0248-0.5010.01-0.19210.0875-0.33330.01030.3674-0.06270.1469-0.0498-0.02170.2261-0.04020.3295-23.443415.097217.7703
301.0395-0.0158-0.01812.2237-0.09290.12850.0515-0.02310.09370.0716-0.02-0.1155-0.0139-0.0642-0.03150.1679-0.00920.01140.1314-0.0010.1572-37.419319.896513.472
313.24770.1233-0.51172.00361.33390.99850.25630.06430.2189-0.1511-0.0951-0.202-0.1334-0.0889-0.16120.2327-0.00010.04550.12460.04570.1431-36.087722.96965.4287
320.13030.35640.02421.21350.24680.24690.0252-0.02370.0155-0.0837-0.05090.02070.00990.01230.02570.22160.0001-0.00920.16010.01260.1399-44.13023.27116.2006
337.4716-2.1442-3.88110.6680.68056.96720.32190.1159-0.1292-0.106-0.0350.1395-0.10640.0044-0.28690.0695-0.0423-0.04240.1184-0.00740.375-60.46090.36748.4146
342.087-1.19850.77491.6078-1.12310.8248-0.0153-0.03560.01090.23360.0370.1568-0.14780.0364-0.02170.19420.00380.06850.14950.05570.2302-49.18170.456117.6073
350.6978-1.460.1543.25480.04850.7755-0.02610.021-0.10650.127-0.04280.31030.05620.00920.06890.1247-0.02410.06340.13270.01150.2281-56.5173-0.339118.5411
366.3064-4.98163.44825.6487-1.71355.4802-0.17780.03620.03230.7825-0.08650.97450.8334-0.11910.26440.3493-0.04590.31160.0197-0.01610.6233-63.9508-7.918221.6212
371.0505-0.3743-0.49980.7237-0.10510.41850.08230.0641-0.11920.0434-0.04140.238-0.03140.0613-0.04090.17410.0152-0.01250.1797-0.00640.2107-50.9611-11.46914.1887
383.23190.3104-2.25714.7984-3.07173.30140.1940.2209-0.3527-0.33550.08580.84070.0666-0.1377-0.27970.0752-0.0539-0.08190.1655-0.06050.2684-58.1846-11.69598.4705
396.6273-2.5143.3271.0285-1.02712.7889-0.13080.2917-0.0340.0971-0.02110.04480.130.23590.1520.18440.0094-0.00540.1989-0.00370.1124-32.96-7.74393.0439
4022.321921.3696-24.099854.54861.328143.4881-1.7878-0.1104-0.2042-1.0211.32740.18522.29611.22760.46030.29650.26150.22720.41760.38460.5058-22.3194-15.65927.7623
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
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