7KI8

Crystal Structure of Dihydrofolate reductase (DHFR) from Mycobacterium ulcerans Agy99 in complex with NADP and inhibitor SDDC-0001580


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6UWWNAD and P218-bound structure, PDB entry 6uww

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5287Microlytic Morpheus screen, condition A5: 10% (w/V) PEG 20000, 20% (v/v) PEG MME 550: 30mM each MgCl2, CaCl2: 100mM MES / imidazole pH 6.5: MyulA.01062.a.B13.PS38558 at 7.98mg/ml + 2.5mM NADP + 2.5mM SDDC-0001580): tray 318200 A1: cryo: direct: puck ucx6-1
Crystal Properties
Matthews coefficientSolvent content
1.8533.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 29.46α = 90
b = 70.86β = 111.41
c = 36.16γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002020-10-01MSINGLE 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
11.2533.6699.50.0560.0660.99812.653.6393806216.438
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)
11.251.2897.80.4240.5220.7742.382.956

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-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTNAD and P218-bound structure, PDB entry 6uww1.2533.661.3738059192699.70.1340.13270.1586016.1988
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 Atoms1243
Nucleic Acid Atoms
Solvent Atoms236
Heterogen Atoms78

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing
PHENIXmodel building
Cootmodel building