4KM2

Crystal structure of Dihydrofolate reductase from Mycobacterium tuberculosis in an open conformation in complex with trimethoprim


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72980.05M KCl, 0.01M MgCl2, 15% PEG 6000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1141.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.16α = 90
b = 65.28β = 90
c = 79.75γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2010-10-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.00000SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)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
11.450.515990.10413.58.9659066590622
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.48980.7710.77118.89385

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.420.996590665797333698.790.14370.14060.2008RANDOM16.479
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]
0.04-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free35.004
r_dihedral_angle_2_deg30.445
r_dihedral_angle_4_deg16.656
r_dihedral_angle_3_deg13.957
r_sphericity_bonded13.709
r_rigid_bond_restr6.899
r_dihedral_angle_1_deg6.715
r_angle_refined_deg2.432
r_chiral_restr0.184
r_bond_refined_d0.024
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free35.004
r_dihedral_angle_2_deg30.445
r_dihedral_angle_4_deg16.656
r_dihedral_angle_3_deg13.957
r_sphericity_bonded13.709
r_rigid_bond_restr6.899
r_dihedral_angle_1_deg6.715
r_angle_refined_deg2.432
r_chiral_restr0.184
r_bond_refined_d0.024
r_gen_planes_refined0.016
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2488
Nucleic Acid Atoms
Solvent Atoms609
Heterogen Atoms104

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
MOSFLMdata reduction
PHASERphasing