6UWW

Crystal structure of dihydrofolate reductase from Mycobacterium ulcerans with P218 inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DF7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5287MORPHEUS E8 (305593e8): 12.5% (w/v) PEG1000, 12.t% (w/v) PEG3350, 12.5% (v/v) MPD, 30mM diethyleneglycol, 30mM triethyleneglycol, 30mM tetraethyleneglycol, 30mM pentaethyleneglycol, 100mM MOPS/HEPES-Na pH7.5, 12.52mg/mL MyulA.01062.a.B11.PS38525, 4mM NADP, 4mM BSI4260, direct cryo, puck id:ogn0-3
Crystal Properties
Matthews coefficientSolvent content
2.2244.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 28.73α = 90
b = 66.2β = 91.614
c = 44.52γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2019-03-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D0.6888APS21-ID-D

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
10.925098.10.0360.0430.99914.663.45111285411.486
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)
10.920.9494.70.4910.6050.7482.012.939

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-VALUE1df70.9244.5021.35112838204998.10.13180.13150.145415.08
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_d12.0297
f_angle_d1.2889
f_chiral_restr0.0863
f_bond_d0.0095
f_plane_restr0.0081
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1304
Nucleic Acid Atoms
Solvent Atoms255
Heterogen Atoms36

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MoRDaphasing