1M7P

Plasmodium Falciparum Triosephosphate isomerase (PfTIM) compled to substrate analog glycerol-3-phosphate (G3P).


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YDVDimer of Unbound PfTIM; PDB code 1YDV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.529512% to 20% PEG 1450 in 100mm Sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP at 295K
Crystal Properties
Matthews coefficientSolvent content
2.2643.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.124α = 90
b = 51.082β = 91.39
c = 89.549γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray295IMAGE PLATEMARRESEARCHMirrors1999-06-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.42096.50.11512.35.11933716.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.42.4996.40.3564.14.81824

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTDimer of Unbound PfTIM; PDB code 1YDV2.4200.117844174992.10.1790.216RANDOM25.5
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]
-2.671.01-1.384.05
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.4
c_scangle_it5.05
c_scbond_it3.39
c_mcangle_it2.8
c_mcbond_it1.85
c_angle_deg1.5
c_improper_angle_d0.97
c_bond_d0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3912
Nucleic Acid Atoms
Solvent Atoms135
Heterogen Atoms20

Software

Software
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling