4YXG

F96Y Mutant of Plasmodium Falciparum Triosephosphate Isomerase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VFH 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829416% PEG 1450, HEPES, 10mM CaCl2, 0.5mM DTT, 0.5mM NaN3, 0.5mM EDTA
Crystal Properties
Matthews coefficientSolvent content
3.663

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37α = 90
b = 70.32β = 101.9
c = 72.58γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2009-06-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.54179

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.936.29915328683
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)
11.92990.2254.33

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 REPLACEMENTTHROUGHOUT2VFH1.935.5127191145499.490.182570.180330.22432RANDOM17.05
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]
0.01-0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.411
r_dihedral_angle_4_deg16.413
r_dihedral_angle_3_deg13.046
r_dihedral_angle_1_deg5.618
r_long_range_B_refined2.244
r_long_range_B_other2.244
r_angle_refined_deg1.034
r_mcangle_it1.024
r_mcangle_other1.023
r_scangle_other0.945
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.411
r_dihedral_angle_4_deg16.413
r_dihedral_angle_3_deg13.046
r_dihedral_angle_1_deg5.618
r_long_range_B_refined2.244
r_long_range_B_other2.244
r_angle_refined_deg1.034
r_mcangle_it1.024
r_mcangle_other1.023
r_scangle_other0.945
r_angle_other_deg0.736
r_mcbond_it0.592
r_mcbond_other0.592
r_scbond_it0.567
r_scbond_other0.567
r_chiral_restr0.061
r_bond_refined_d0.005
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3614
Nucleic Acid Atoms
Solvent Atoms170
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing