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- PDB-4h4d: IspH in complex with (E)-4-amino-3-methylbut-2-enyl diphosphate -

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Basic information

Entry
Database: PDB / ID: 4h4d
TitleIspH in complex with (E)-4-amino-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-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-10E / 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: 1.35 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_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)72,5766
Polymers71,3512
Non-polymers1,2254
Water13,169731
1
A: 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2883
Polymers35,6751
Non-polymers6132
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)36,2883
Polymers35,6751
Non-polymers6132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.320, 80.710, 112.110
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(-0.999358, 0.010107, 0.03436), (0.0106, 0.999843, 0.0142), (-0.034211, 0.014556, -0.999309)-66.78647, 0.51019, -1.54392

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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-10E / (2E)-4-amino-3-methylbut-2-en-1-yl trihydrogen diphosphate


Mass: 261.107 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H13NO7P2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 731 / 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: 2.26 Å3/Da / Density % sol: 45.6 %
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: 1.35→30 Å / Num. all: 142270 / Num. obs: 139140 / % possible obs: 97.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rsym value: 0.058 / Net I/σ(I): 11
Reflection shellResolution: 1.35→1.45 Å / Mean I/σ(I) obs: 3.1 / Rsym value: 0.497 / % possible all: 98.1

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Processing

Software
NameVersionClassification
XDSdata scaling
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KE8
Resolution: 1.35→10 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.827 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21441 6938 5 %RANDOM
Rwork0.19054 ---
obs0.19174 131832 97.59 %-
all-139139 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.627 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å2-0 Å20 Å2
2---0.35 Å2-0 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.35→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4773 0 46 731 5550
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0194897
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3521.9776648
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6645617
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.57824.159226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.28515853
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4391544
X-RAY DIFFRACTIONr_chiral_restr0.1610.2764
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0213674
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: 2391 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.420.5
MEDIUM THERMAL2.072
LS refinement shellResolution: 1.35→1.384 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 498 -
Rwork0.248 9478 -
obs--97.46 %
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)
12.05940.0589-0.38460.12860.1410.2587-0.0591-0.0586-0.10340.0440.0279-0.00450.05570.03260.03120.07970.0108-0.02230.09980.00660.0734-9.262-7.8869-7.7134
21.01820.73240.16170.55830.09630.03910.0271-0.0803-0.0658-0.0262-0.0266-0.05830.0296-0.0385-0.00050.088-0.0094-0.00560.1143-0.01430.0521-30.0518-10.0496-11.2893
30.28710.24140.37370.48430.70831.11250.03550.0618-0.0223-0.0597-0.08970.03910.003-0.10810.05420.14050.0367-0.02470.1287-0.02790.0343-40.3495-12.9453-22.3457
42.28460.06080.56841.35890.79710.59230.0228-0.0108-0.103-0.08550.0246-0.0483-0.04730.0071-0.04730.09460.00170.00250.1026-0.00970.0357-26.8722-10.0909-22.0022
53.167-2.4650.7354.8249-0.05750.26190.07580.3107-0.0792-0.3785-0.06120.036-0.04540.1005-0.01460.1280.022-0.03110.1292-0.01970.0138-37.5007-8.9572-28.1559
60.1014-0.30740.0241.00730.00870.09650.03590.0302-0.0328-0.1122-0.07460.1454-0.00370.02420.03860.08580.0104-0.03010.1241-0.02280.0642-41.3002-4.3942-21.1957
71.24581.10850.70446.63121.79460.6409-0.06110.01340.1056-0.1698-0.07450.5091-0.052-0.00240.13550.04870.008-0.06580.1105-0.02620.1037-48.66580.1575-23.2054
80.86950.17470.01880.34850.13670.0585-0.027-0.00570.00470.0609-0.00110.08760.0338-0.00040.02810.07240.0048-0.00910.1113-0.01250.065-39.3126-0.2937-12.2293
90.3197-0.66920.5395.8667-0.72430.94920.00350.009-0.01210.2058-0.01230.4540.02020.02970.00880.02820.00940.02430.0841-0.02030.1471-44.117115.8005-9.8227
100.0929-0.4043-0.10092.00560.43690.10970.00470.00210.0104-0.12580.00880.0592-0.00620.0015-0.01360.10030.0081-0.02340.10450.00360.0531-31.045512.157-17.6919
110.4980.17030.09331.1983-0.03920.11990.00470.05630.02-0.087-0.02660.1128-0.06880.00350.02190.08140.0162-0.02150.09030.00710.0521-34.439821.1952-16.6708
120.3234-0.01620.07621.3105-0.20160.04990.0144-0.01850.02340.0437-0.0192-0.0570.002-0.00760.00480.08840.0055-0.01060.0929-0.00720.0563-24.233514.4788-10.2754
130.7813-0.01720.26340.7253-0.70440.76290.0207-0.03330.08940.02220.00610.0589-0.0102-0.0081-0.02680.10610.00610.0090.0889-0.01430.0435-29.550222.9041-5.4861
140.4862-0.3449-0.11550.6431-0.11440.12780.0071-0.0230.01760.0393-0.0109-0.0347-0.01020.00790.00370.08120.0009-0.01670.1055-0.00450.0586-19.59932.965-5.9341
150.82930.24870.02060.23710.10810.07610.02260.02630.0349-0.0348-0.0036-0.0664-0.0246-0.0258-0.0190.0671-0.00430.00430.0896-0.00510.1088-11.6150.5053-15.9028
161.3067-0.02580.22190.88711.00532.0828-0.01460.0269-0.0568-0.13260.0896-0.17330.09110.1651-0.0750.08970.00690.05350.0773-0.00310.1055-2.6602-8.3585-20.6394
170.0531-0.10390.01560.2427-0.00320.14010.0126-0.02060.0027-0.00450.0029-0.04590.033-0.0393-0.01560.0760.0062-0.00880.09250.0040.0862-14.8327-11.5139-13.7085
180.4609-0.6413-0.4352.05442.18112.59540.0554-0.0657-0.05440.2003-0.0053-0.03930.325-0.115-0.05010.09150.0017-0.01170.1150.00240.0842-7.7733-11.7703-7.748
192.50050.21330.88190.13390.39571.2182-0.1222-0.1383-0.207-0.00870.00440.0452-0.0393-0.06690.11780.0695-0.00210.00040.1398-0.01190.0609-32.0914-7.2644-2.4264
2014.30659.11990.10398.34071.7951.18340.508-0.65170.03320.1037-0.97950.7-0.1449-0.3940.47150.0596-0.0073-0.05380.2053-0.15910.1828-44.4858-13.6513-8.6157
210.7233-0.2967-0.2420.15710.00230.351-0.02630.0957-0.0425-0.0056-0.01870.00880.0601-0.070.0450.0775-0.01660.00130.1139-0.01550.0606-57.1409-8.06947.9713
220.7574-0.42740.16250.3498-0.20430.18590.00470.0217-0.02220.02170.00220.00150.03040.0023-0.0070.1007-0.0003-0.01950.08790.00490.0531-34.1334-11.318117.6532
235.2959-1.8317-0.14880.7575-0.26440.8215-0.0647-0.21460.01510.05180.13410.0137-0.0441-0.1132-0.06950.0980.0022-0.05740.1065-0.00530.0768-34.1193-18.160525.4324
240.1603-0.14950.06520.2175-0.17610.26120.03690.0066-0.0043-0.00730.0087-0.0031-0.00320.0398-0.04560.0743-0.0004-0.03860.1036-0.01680.0726-25.2095-6.094224.7533
250.1418-0.76430.21084.4536-0.94550.5765-0.02370.02660.06910.0144-0.1443-0.2781-0.00260.0060.16810.0724-0.0141-0.02910.08630.02220.1044-18.76492.076320.5714
260.3986-0.25010.49520.2364-0.40180.7265-0.02430.0825-0.008-0.02220.004-0.03210.02630.05110.02030.07410.0046-0.01110.117-0.01530.0781-23.681-4.152215.546
270.26790.4793-0.31972.47790.04240.66940.01990.0152-0.0195-0.0359-0.0721-0.1711-0.0027-0.03650.05210.0502-0.0030.020.09060.04820.161-24.052612.36768.9988
280.37020.1414-0.15151.5398-0.51890.206-0.035-0.00950.09360.1490.0165-0.1552-0.0298-0.00930.01850.0965-0.0138-0.02580.0830.00070.0774-33.588913.286916.7044
290.09050.01750.21940.00590.04990.5929-0.0196-0.0060.04690.0068-0.0133-0.00850.02950.02750.03290.07810.0052-0.06980.0932-0.01790.1598-24.321715.121117.9004
300.4299-0.11160.1431.4859-0.17240.0665-0.02410.00660.03260.1110.0146-0.1049-0.014-0.02070.00950.0888-0.0045-0.00050.08550.00770.069-38.234719.785313.3545
310.8923-0.10850.20821.36451.06730.93290.070.04860.14-0.0674-0.0382-0.1047-0.0279-0.0227-0.03180.1098-0.00110.02440.07880.00780.062-36.676422.87485.3003
320.25160.4312-0.02551.02120.23760.2890.00130.0293-0.0044-0.0192-0.0006-0.0163-0.0103-0.0351-0.00070.07730.0008-0.00090.11160.00890.0506-44.78133.21345.9814
333.0506-0.0636-1.4861.7128-1.53832.16320.04730.1980.06980.01960.10880.1288-0.04-0.1947-0.15610.028-0.00320.0070.1197-0.00720.0873-61.13660.04548.1122
340.8378-0.1041-0.10970.2084-0.16870.19470.0051-0.01710.01070.070.00860.0296-0.047-0.0046-0.01370.0927-0.00030.01550.10310.00640.0523-49.81380.252117.3676
350.8434-0.6687-0.09861.8345-0.55230.32820.0196-0.0068-0.01020.09140.00960.113-0.0291-0.0096-0.02920.07820.00220.03340.0943-0.00320.0625-57.1874-0.611218.2725
362.4324-0.50112.03580.6173-1.38084.5973-0.1967-0.06250.08550.1120.03740.1490.1312-0.23210.15930.1939-0.0440.17290.0997-0.02710.206-64.5978-8.531821.0877
370.4188-0.1159-0.21130.4710.1240.1191-0.02290.0514-0.02870.04570.00980.02580.0168-0.00770.01310.0733-0.01070.0070.09440.00160.0751-51.4101-11.691413.8244
381.730.8066-1.15771.6494-1.48351.9466-0.09860.2132-0.2576-0.09690.03710.07860.1344-0.1570.06150.0359-0.03730.01030.1077-0.04090.073-58.5303-11.85777.984
390.8923-0.14730.82540.5273-0.22620.8616-0.03990.1228-0.0625-0.01020.0309-0.02420.0070.0810.0090.06960.00140.02070.1344-0.01310.0598-33.5399-7.66582.7845
407.2375.98915.19826.33924.58426.5155-0.03790.4111-0.03-0.2598-0.4523-0.87691.14870.89930.49020.50240.2670.23150.18850.14570.1329-23.3897-15.9247.5162
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
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