2VFI

Crystal structure of the Plasmodium falciparum triosephosphate isomerase in the loop closed state with 3-phosphoglycerate bound at the active site and 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
2.143.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.611α = 90
b = 51.135β = 98.24
c = 92.185γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHOSMIC MIRROR2006-12-10MSINGLE 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
12.255095.10.19.22.62259828.8
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)
12.252.3380.50.382.31.82

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 1O5X2.2591.2921429115595.130.211670.208910.26022RANDOM22.8
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]
-0.38-0.15-0.320.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.39
r_dihedral_angle_4_deg16.476
r_dihedral_angle_3_deg14.937
r_dihedral_angle_1_deg4.949
r_angle_refined_deg0.968
r_scangle_it0.592
r_scbond_it0.357
r_mcangle_it0.34
r_nbtor_refined0.292
r_mcbond_it0.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.39
r_dihedral_angle_4_deg16.476
r_dihedral_angle_3_deg14.937
r_dihedral_angle_1_deg4.949
r_angle_refined_deg0.968
r_scangle_it0.592
r_scbond_it0.357
r_mcangle_it0.34
r_nbtor_refined0.292
r_mcbond_it0.19
r_nbd_refined0.155
r_symmetry_vdw_refined0.113
r_xyhbond_nbd_refined0.107
r_symmetry_hbond_refined0.076
r_chiral_restr0.061
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 Atoms3907
Nucleic Acid Atoms
Solvent Atoms353
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing