7T93

Crystal Structure of Fumarate hydratase class II from Mycobacterium ulcerans in complex with L-Malate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3QBP 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5287[Protein: MyulA.01507.a.A1.PW29760 25mg/mL] [Barcode: 321232f4] [Collection: aps21idf 9/23/21] [Crystallization conditions: Molecular Dimensions Morpheus sparse matrix screen, condition F4: 0.1M MES/Imidazole pH 6.5, 12.5%(w/v) PEG 1000, 12.5%(w/v) PEG 3350, 12.5%(v/v) MPD, 0.02M each of (D-glucose, D-mannose, D-galactose, L-fucose, D-xylose, N-acetyl-D-glusosamine)] [Cryo: Direct]
Crystal Properties
Matthews coefficientSolvent content
2.2445.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.04α = 90
b = 120.82β = 90
c = 158.78γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-300Beryllium Lenses2021-09-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.6548.4899.90.1090.1180.99811.916.21922558611.63
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.651.6999.60.5530.6020.8983.256.203

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3QBP1.6548.481.34225518202099.840.13780.13760.160715.9495
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13511
Nucleic Acid Atoms
Solvent Atoms2207
Heterogen Atoms62

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MoRDaphasing