2VFF

Crystal structure of the F96H mutant of Plasmodium falciparum triosephosphate isomerase


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
2.143.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.514α = 90
b = 50.778β = 92.38
c = 89.155γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHOSMIC MIRROR2006-08-10MSINGLE 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
11.75093.80.0520.12.374971022.6
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)
11.71.7681.20.234.42.13

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 1O5X1.722.5147961256495.10.19420.192630.22309RANDOM19.59
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]
-0.03-0.010.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.97
r_dihedral_angle_3_deg11.64
r_dihedral_angle_4_deg11.345
r_dihedral_angle_1_deg5.366
r_scangle_it2.019
r_scbond_it1.309
r_angle_refined_deg0.998
r_mcangle_it0.752
r_mcbond_it0.473
r_nbtor_refined0.299
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.97
r_dihedral_angle_3_deg11.64
r_dihedral_angle_4_deg11.345
r_dihedral_angle_1_deg5.366
r_scangle_it2.019
r_scbond_it1.309
r_angle_refined_deg0.998
r_mcangle_it0.752
r_mcbond_it0.473
r_nbtor_refined0.299
r_nbd_refined0.179
r_symmetry_vdw_refined0.166
r_xyhbond_nbd_refined0.116
r_symmetry_hbond_refined0.108
r_chiral_restr0.067
r_bond_refined_d0.008
r_gen_planes_refined0.004
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 Atoms3890
Nucleic Acid Atoms
Solvent Atoms527
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing