8C53

Trypanosoma brucei IMP dehydrogenase (ori) crystallized in High Five cells reveals native ligands ATP, GDP and phosphate. Diffraction data collection at 100 K in cellulo; CrystFEL processing


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1IN CELL300crystallized in rBV Tb IMPDH ori (MOI 1) infected High Five cells, in adhesion culture using ESF921 cell culture medium.
Crystal Properties
Matthews coefficientSolvent content
4.4372.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 206.9α = 90
b = 206.9β = 90
c = 92.3γ = 90
Symmetry
Space GroupP 4 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 S 16M2019-11-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)0.987PETRA III, EMBL c/o DESYP14 (MX2)

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1mesh mountsfixed target
Fixed Target
Diffraction IDDescriptionSample HoldingSupport BaseMotion controlSample Solvent
1mesh gridgoniometer
Data Reduction
Diffraction IDFrames IndexedCrystal HitsTotal Frames
17574196949

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)R Split (All)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
12.29957.3899.880.99760.086210.0636678907052.99
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)R Split (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.2992.3399.090.19571.99521246

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 REPLACEMENTFREE R-VALUE1JCN2.357.381.3388954107899.920.20870.20830.2428
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d7.996
f_angle_d0.727
f_chiral_restr0.044
f_bond_d0.006
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6731
Nucleic Acid Atoms
Solvent Atoms150
Heterogen Atoms128

Software

Software
Software NamePurpose
PHENIXrefinement
MxCuBEdata collection
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing