5BRB

Crystal structure of Q64E mutant of Triosephosphate isomerase from Plasmodium falciparum


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29628% PEG 1450, 100mM HEPES, 10mM calcium chloride, 0.5mM DTT, 0.5mM sodium azide
Crystal Properties
Matthews coefficientSolvent content
1.9436.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.02α = 90
b = 75.35β = 97.72
c = 74.13γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2013-09-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.541

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
12.52675.3597.20.1560.1870.1015.63.2142041420440
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.512.6581.40.4410.4410.2982.331734

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 REPLACEMENTTHROUGHOUT1O5X2.5373.571347471498.50.2320.22880.2927RANDOM23.718
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]
-0.92-0.63-0.341.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.058
r_dihedral_angle_4_deg13.232
r_dihedral_angle_3_deg12.491
r_dihedral_angle_1_deg5.8
r_angle_refined_deg1.07
r_angle_other_deg0.87
r_mcangle_it0.714
r_mcbond_it0.407
r_mcbond_other0.406
r_chiral_restr0.057
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.058
r_dihedral_angle_4_deg13.232
r_dihedral_angle_3_deg12.491
r_dihedral_angle_1_deg5.8
r_angle_refined_deg1.07
r_angle_other_deg0.87
r_mcangle_it0.714
r_mcbond_it0.407
r_mcbond_other0.406
r_chiral_restr0.057
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3667
Nucleic Acid Atoms
Solvent Atoms69
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
PHASERphasing