5U26

Crystal Structure of Mycobacterium tuberculosis Dihydrofolate Reductase Bound to NADP and p218 Inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7DFR 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5289Mycobacterium tuberculosis DHFR, R9978 at 10 mg/ml, Batch number BOS051006 against RigakuReagents Ammonium Sulfate Screen, condition B10: 2.2M ammonium sulfate + 0.2M potassium acetate; 20% EG cryo; crystal tracking ID 255057b10 (puck gel2-3)
Crystal Properties
Matthews coefficientSolvent content
1.9332

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 29.05α = 90
b = 66.98β = 90
c = 77.26γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2014-06-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.855096.10.0980.99923.2415.412959-314.39
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.986.80.5820.9014.328817

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-VALUE7DFR1.8533.4631.361295964596.090.15010.14790.191517.0744
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_d18.187
f_angle_d1.724
f_chiral_restr0.089
f_bond_d0.018
f_plane_restr0.015
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1277
Nucleic Acid Atoms
Solvent Atoms124
Heterogen Atoms88

Software

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