1XIQ

Plasmodium falciparum Nucleoside diphosphate kinase B


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5298calcium acetate, PEG3350, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.345.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.593α = 90
b = 112.424β = 119.05
c = 68.59γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42004-06-10MSINGLE WAVELENGTH
21100CCDADSC QUANTUM 2102004-06-20
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.974609SSRLBL11-1
2SYNCHROTRONALS BEAMLINE 8.2.10.9793ALS8.2.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
13.0552.70599.440.1110.1117.13.51742417326-380.965
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.053.21990.5740.5741.93.42519

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT3.0552.7174241644787699.470.232380.232380.229480.28608RANDOM50.431
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]
-0.22-0.170.22-0.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg4.823
r_scangle_it4.515
r_mcangle_it3.002
r_scbond_it2.836
r_mcbond_it1.618
r_angle_refined_deg1.156
r_nbd_refined0.211
r_symmetry_vdw_refined0.205
r_xyhbond_nbd_refined0.16
r_symmetry_hbond_refined0.102
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg4.823
r_scangle_it4.515
r_mcangle_it3.002
r_scbond_it2.836
r_mcbond_it1.618
r_angle_refined_deg1.156
r_nbd_refined0.211
r_symmetry_vdw_refined0.205
r_xyhbond_nbd_refined0.16
r_symmetry_hbond_refined0.102
r_chiral_restr0.086
r_bond_refined_d0.011
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7164
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
SHARPphasing