2WWF

Plasmodium falciparum thymidylate kinase in complex with TMP and ADP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1E2QPDB ENTRY 1E2Q

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.575 MM HEPES PH 7.5, 1.35 M TRI- SODIUM CITRATE, 0.125 M NACL
Crystal Properties
Matthews coefficientSolvent content
2.9858.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.127α = 90
b = 110.127β = 90
c = 120.097γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2007-04-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-1ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.94094.30.0817.45.167190
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.9347.40.32.22

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1E2Q1.8995.3560137319894.30.1630.160.203RANDOM19.96
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]
0.50.250.5-0.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.298
r_dihedral_angle_4_deg28.989
r_dihedral_angle_3_deg14.98
r_dihedral_angle_1_deg5.734
r_scangle_it5.337
r_scbond_it3.45
r_mcangle_it2.058
r_angle_refined_deg2.007
r_mcbond_it1.144
r_chiral_restr0.224
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.298
r_dihedral_angle_4_deg28.989
r_dihedral_angle_3_deg14.98
r_dihedral_angle_1_deg5.734
r_scangle_it5.337
r_scbond_it3.45
r_mcangle_it2.058
r_angle_refined_deg2.007
r_mcbond_it1.144
r_chiral_restr0.224
r_bond_refined_d0.025
r_gen_planes_refined0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5240
Nucleic Acid Atoms
Solvent Atoms489
Heterogen Atoms205

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing