4ZZ9

Crystal structure of T75S 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 DROP729622% PEG 1450, 100 mM HEPES buffer, 10 mM Calcium chloride, 0.5 mM EDTA, 0.5 mM DTT, 0.5 mM sodium azide
Crystal Properties
Matthews coefficientSolvent content
238.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.23α = 90
b = 76.54β = 98.27
c = 74.94γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2014-04-15MSINGLE 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
11.80574.16199.90.10.1140.05410.14.3403174031717.826
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)
11.81.999.50.480.480.2682.84.15839

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 REPLACEMENTTHROUGHOUT1O5X1.8174.1638249202099.760.178230.175090.23686RANDOM15.609
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]
0.18-0.01-0.460.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.82
r_dihedral_angle_4_deg14.906
r_dihedral_angle_3_deg12.875
r_dihedral_angle_1_deg6.28
r_long_range_B_refined4.466
r_scbond_it1.817
r_angle_refined_deg1.76
r_mcangle_it1.658
r_mcbond_it1.146
r_chiral_restr0.122
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.82
r_dihedral_angle_4_deg14.906
r_dihedral_angle_3_deg12.875
r_dihedral_angle_1_deg6.28
r_long_range_B_refined4.466
r_scbond_it1.817
r_angle_refined_deg1.76
r_mcangle_it1.658
r_mcbond_it1.146
r_chiral_restr0.122
r_bond_refined_d0.018
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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_it
r_scangle_other
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 Atoms3836
Nucleic Acid Atoms
Solvent Atoms522
Heterogen Atoms18

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
PHASERphasing