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- PDB-4bi5: CRYSTAL STRUCTURE OF A DOUBLE MUTANT (C202A AND C222D) OF TRIOSEP... -

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Entry
Database: PDB / ID: 4bi5
TitleCRYSTAL STRUCTURE OF A DOUBLE MUTANT (C202A AND C222D) OF TRIOSEPHOSPHATE ISOMERASE FROM GIARDIA LAMBLIA.
ComponentsTRIOSEPHOSPHATE ISOMERASE
KeywordsISOMERASE
Function / homology
Function and homology information


methylglyoxal synthase / methylglyoxal synthase activity / triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / gluconeogenesis / glycolytic process / cytosol
Similarity search - Function
Triosephosphate isomerase, bacterial/eukaryotic / Triosephosphate isomerase, active site / Triosephosphate isomerase active site. / Triosephosphate isomerase / Triosephosphate isomerase superfamily / Triosephosphate isomerase / Triosephosphate isomerase (TIM) family profile. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel ...Triosephosphate isomerase, bacterial/eukaryotic / Triosephosphate isomerase, active site / Triosephosphate isomerase active site. / Triosephosphate isomerase / Triosephosphate isomerase superfamily / Triosephosphate isomerase / Triosephosphate isomerase (TIM) family profile. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Triosephosphate isomerase
Similarity search - Component
Biological speciesGIARDIA INTESTINALIS (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsTorres-Larios, A. / Enriquez-Flores, S. / Reyes-Vivas, H. / Oria-Hernandez, J. / Hernandez-Alcantara, G.
CitationJournal: Plos One / Year: 2013
Title: Structural and Functional Perturbation of Giardia Lamblia Triosephosphate Isomerase by Modification of a Non-Catalytic, Non-Conserved Region.
Authors: Hernandez-Alcantara, G. / Torres-Larios, A. / Enriquez-Flores, S. / Garcia-Torres, I. / Castillo-Villanueva, A. / Mendez, S.T. / De La Mora-De La Mora, I. / Gomez-Manzo, S. / Torres-Arroyo, ...Authors: Hernandez-Alcantara, G. / Torres-Larios, A. / Enriquez-Flores, S. / Garcia-Torres, I. / Castillo-Villanueva, A. / Mendez, S.T. / De La Mora-De La Mora, I. / Gomez-Manzo, S. / Torres-Arroyo, A. / Lopez-Velazquez, G. / Reyes-Vivas, H. / Oria-Hernandez, J.
History
DepositionApr 9, 2013Deposition site: PDBE / Processing site: PDBE
SupersessionJun 5, 2013ID: 2YC8
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "FA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "GA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "HA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "IA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "JA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "KA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "LA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "MA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "PA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "QA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "RA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "SA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "TA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRIOSEPHOSPHATE ISOMERASE
B: TRIOSEPHOSPHATE ISOMERASE
C: TRIOSEPHOSPHATE ISOMERASE
D: TRIOSEPHOSPHATE ISOMERASE
E: TRIOSEPHOSPHATE ISOMERASE
F: TRIOSEPHOSPHATE ISOMERASE
G: TRIOSEPHOSPHATE ISOMERASE
H: TRIOSEPHOSPHATE ISOMERASE
I: TRIOSEPHOSPHATE ISOMERASE
J: TRIOSEPHOSPHATE ISOMERASE
K: TRIOSEPHOSPHATE ISOMERASE
L: TRIOSEPHOSPHATE ISOMERASE
M: TRIOSEPHOSPHATE ISOMERASE
N: TRIOSEPHOSPHATE ISOMERASE
O: TRIOSEPHOSPHATE ISOMERASE
P: TRIOSEPHOSPHATE ISOMERASE
Q: TRIOSEPHOSPHATE ISOMERASE
R: TRIOSEPHOSPHATE ISOMERASE
S: TRIOSEPHOSPHATE ISOMERASE
T: TRIOSEPHOSPHATE ISOMERASE


Theoretical massNumber of molelcules
Total (without water)553,23520
Polymers553,23520
Non-polymers00
Water00
1
O: TRIOSEPHOSPHATE ISOMERASE
P: TRIOSEPHOSPHATE ISOMERASE


Theoretical massNumber of molelcules
Total (without water)55,3242
Polymers55,3242
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-25.7 kcal/mol
Surface area19850 Å2
MethodPISA
2
G: TRIOSEPHOSPHATE ISOMERASE
H: TRIOSEPHOSPHATE ISOMERASE


Theoretical massNumber of molelcules
Total (without water)55,3242
Polymers55,3242
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-24.3 kcal/mol
Surface area20190 Å2
MethodPISA
3
E: TRIOSEPHOSPHATE ISOMERASE
F: TRIOSEPHOSPHATE ISOMERASE


Theoretical massNumber of molelcules
Total (without water)55,3242
Polymers55,3242
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-25.6 kcal/mol
Surface area20010 Å2
MethodPISA
4
A: TRIOSEPHOSPHATE ISOMERASE
B: TRIOSEPHOSPHATE ISOMERASE


Theoretical massNumber of molelcules
Total (without water)55,3242
Polymers55,3242
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-24.6 kcal/mol
Surface area20060 Å2
MethodPISA
5
K: TRIOSEPHOSPHATE ISOMERASE
L: TRIOSEPHOSPHATE ISOMERASE


Theoretical massNumber of molelcules
Total (without water)55,3242
Polymers55,3242
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-24.9 kcal/mol
Surface area20020 Å2
MethodPISA
6
M: TRIOSEPHOSPHATE ISOMERASE
N: TRIOSEPHOSPHATE ISOMERASE


Theoretical massNumber of molelcules
Total (without water)55,3242
Polymers55,3242
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-25.1 kcal/mol
Surface area19900 Å2
MethodPISA
7
I: TRIOSEPHOSPHATE ISOMERASE
J: TRIOSEPHOSPHATE ISOMERASE


Theoretical massNumber of molelcules
Total (without water)55,3242
Polymers55,3242
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-23.8 kcal/mol
Surface area20130 Å2
MethodPISA
8
C: TRIOSEPHOSPHATE ISOMERASE
D: TRIOSEPHOSPHATE ISOMERASE


Theoretical massNumber of molelcules
Total (without water)55,3242
Polymers55,3242
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-22.4 kcal/mol
Surface area19850 Å2
MethodPISA
9
S: TRIOSEPHOSPHATE ISOMERASE
T: TRIOSEPHOSPHATE ISOMERASE


Theoretical massNumber of molelcules
Total (without water)55,3242
Polymers55,3242
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-23.6 kcal/mol
Surface area20280 Å2
MethodPISA
10
Q: TRIOSEPHOSPHATE ISOMERASE
R: TRIOSEPHOSPHATE ISOMERASE


Theoretical massNumber of molelcules
Total (without water)55,3242
Polymers55,3242
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-23.8 kcal/mol
Surface area20460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.219, 131.566, 132.549
Angle α, β, γ (deg.)115.73, 89.81, 90.24
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9967, 0.0412, -0.0703), (0.0374, -0.5355, -0.8437), (-0.0724, -0.8435, 0.5322)62.5262, 82.0834, 48.0543
2given(-0.9996, -0.0227, 0.0175), (0.0256, -0.4307, 0.9021), (-0.0129, 0.9022, 0.4311)54.6026, -63.4444, 39.6248
3given(0.9976, -0.0673, -0.0139), (-0.0477, -0.5318, -0.8455), (0.0495, 0.8442, -0.5337)2.5215, 84.6498, 118.6562
4given(-0.9763, -0.1955, -0.0925), (0.183, -0.519, -0.8349), (0.1153, -0.8321, 0.5425)15.786, 81.1916, 9.6455
5given(0.9715, 0.2363, 0.018), (-0.2362, 0.9717, -0.0076), (-0.0193, 0.0031, 0.9998)49.477, 30.6287, -16.2743
6given(-0.9966, -0.047, 0.0673), (0.0318, 0.5354, 0.844), (-0.0757, 0.8433, -0.5321)7.5953, 4.1913, 39.8887
7given(1, 0.0051, 0.0014), (0.0052, -1, -0.0034), (0.0013, 0.0034, -1)52.4134, 46.4829, 65.0827
8given(0.9972, 0.0735, 0.0122), (-0.0495, 0.5309, 0.846), (0.0558, -0.8442, 0.5331)53.42, -67.8445, 13.4163
9given(-0.9997, 0.0135, -0.0182), (0.0222, 0.4312, -0.902), (-0.0043, -0.9021, -0.4314)5.6666, 109.2015, 108.4978
10given(0.9869, -0.0211, -0.1602), (-0.1471, -0.5276, -0.8367), (-0.0668, 0.8492, -0.5237)74.3345, 142.8006, 34.4168
11given(-0.9852, -0.0557, 0.1621), (0.1702, -0.4272, 0.888), (0.0198, 0.9024, 0.4304)-8.5246, -21.561, -58.8712
12given(0.9713, -0.237, -0.0173), (-0.2369, -0.9715, 0.0068), (-0.0184, -0.0025, -0.9998)-1.2407, 30.7759, 169.1742
13given(-0.9767, 0.1936, 0.0921), (0.1817, 0.5195, 0.835), (0.1139, 0.8323, -0.5426)52.5743, -76.6739, 113.186
14given(0.9868, 0.0327, 0.1589), (-0.1521, 0.5261, 0.8367), (-0.0562, -0.8498, 0.5241)-10.2487, -67.0078, 43.1329
15given(-0.9861, 0.0434, -0.1605), (0.1635, 0.4272, -0.8893), (0.0299, -0.9031, -0.4283)67.1628, 82.3976, 127.5987
16given(-0.9913, 0.1182, -0.0583), (-0.1205, -0.992, 0.0369), (-0.0535, 0.0436, 0.9976)62.3872, 12.8913, 7.0503
17given(0.9886, -0.1504, 0.0061), (0.0757, 0.4617, -0.8838), (0.1301, 0.8742, 0.4679)0.0524, 71.2304, 38.6018
18given(-0.991, -0.1238, 0.0499), (-0.1259, 0.9913, -0.0397), (-0.0445, -0.0456, -0.998)12.1271, -36.9207, 71.5452
19given(0.9875, 0.1576, -0.0056), (0.0783, -0.4589, 0.885), (0.1369, -0.8744, -0.4655)45.4513, 38.9502, 116.5613

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Components

#1: Protein
TRIOSEPHOSPHATE ISOMERASE / TIM / TRIOSE-PHOSPHATE ISOMERASE


Mass: 27661.770 Da / Num. of mol.: 20 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GIARDIA INTESTINALIS (eukaryote) / Strain: WB / Plasmid: PET3A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYS / References: UniProt: P36186, triose-phosphate isomerase

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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: 2.98 Å3/Da / Density % sol: 58.8 % / Description: NONE
Crystal growpH: 6.5
Details: PROTEIN WAS CRYSTALLIZED FROM 0.05 M CESIUM CHLORIDE, 0.1 M MES MONOHYDRATE PH 6.5, 30% V/V JEFFAMINE M-600

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97857
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 5, 2009 / Details: MIRRORS
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.7→79.01 Å / Num. obs: 147201 / % possible obs: 82 % / Observed criterion σ(I): 13 / Redundancy: 2.85 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 5.7
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 1.4 / % possible all: 82

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERFOR MRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DP3

2dp3


Resolution: 2.7→78.87 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.863 / Cross valid method: THROUGHOUT / ESU R Free: 0.424 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.27232 7212 5 %RANDOM
Rwork0.23933 ---
obs0.24098 136985 82.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.108 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.7→78.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms38560 0 0 0 38560
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02239200
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9471.94952880
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.87355060
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.2924.6911620
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.4157040
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.03715220
X-RAY DIFFRACTIONr_chiral_restr0.0620.26000
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02128920
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_it4.7131.525060
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.295240100
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.105314140
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.8184.512780
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.409 544 -
Rwork0.36 10467 -
obs--84.94 %

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