2VFG

Crystal structure of the F96H mutant of Plasmodium falciparum triosephosphate isomerase with 3-phosphoglycerate bound at the dimer interface


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1O5XPDB ENTRY 1O5X

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
150.1 M SODIUM ACETATE PH 4.0-5.5, PEG 1450 8-24%
Crystal Properties
Matthews coefficientSolvent content
2.0941.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.197α = 90
b = 47.136β = 96.65
c = 109.167γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHOSMIC MIRROR2006-08-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU200

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
11.955093.30.19.82.76225624
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)
11.952.0282.30.441.972.03

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 1O5X1.9523.7855242296387.040.210280.208280.24819RANDOM21.326
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]
0.24-0.12-0.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.677
r_dihedral_angle_3_deg12.559
r_dihedral_angle_4_deg9.981
r_dihedral_angle_1_deg4.567
r_angle_refined_deg0.874
r_scangle_it0.433
r_mcangle_it0.295
r_nbtor_refined0.289
r_scbond_it0.278
r_mcbond_it0.166
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.677
r_dihedral_angle_3_deg12.559
r_dihedral_angle_4_deg9.981
r_dihedral_angle_1_deg4.567
r_angle_refined_deg0.874
r_scangle_it0.433
r_mcangle_it0.295
r_nbtor_refined0.289
r_scbond_it0.278
r_mcbond_it0.166
r_nbd_refined0.148
r_symmetry_vdw_refined0.146
r_xyhbond_nbd_refined0.092
r_symmetry_hbond_refined0.062
r_chiral_restr0.056
r_bond_refined_d0.006
r_gen_planes_refined0.002
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
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 Atoms7705
Nucleic Acid Atoms
Solvent Atoms677
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing