5BMW

Crystal structure of T75V 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 DROP6.529620% PEG 1450, 100 mM MES buffer, 10 mM Calcium chloride, 0.5 mM EDTA, 0.5 mM DTT, 0.5 mM sodium azide
Crystal Properties
Matthews coefficientSolvent content
1.9737.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.21α = 90
b = 76.02β = 97.47
c = 74.36γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2014-04-10MSINGLE 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
11.85973.7399.80.0560.0610.02522.25.63639236392
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)
11.861.9698.40.1560.1560.0754.75.25211

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 REPLACEMENTTHROUGHOUT1O5X1.8673.7334547181699.740.1340.13140.1824RANDOM11.586
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]
0.22-0.02-0.16-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.944
r_dihedral_angle_3_deg11.758
r_dihedral_angle_4_deg11.258
r_dihedral_angle_1_deg6.47
r_angle_refined_deg1.802
r_mcangle_it1.303
r_angle_other_deg1.033
r_mcbond_it0.896
r_mcbond_other0.89
r_chiral_restr0.111
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.944
r_dihedral_angle_3_deg11.758
r_dihedral_angle_4_deg11.258
r_dihedral_angle_1_deg6.47
r_angle_refined_deg1.802
r_mcangle_it1.303
r_angle_other_deg1.033
r_mcbond_it0.896
r_mcbond_other0.89
r_chiral_restr0.111
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3859
Nucleic Acid Atoms
Solvent Atoms483
Heterogen Atoms47

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
PHASERphasing