5YIE

Crystal Structure of KNI-10742 bound Plasmepsin II (PMII) from Plasmodium falciparum


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52950.1 M HEPES pH 7.5, 1.4 M sodium citrate tribasic dihydrate
Crystal Properties
Matthews coefficientSolvent content
2.7955.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.6α = 90
b = 106.6β = 90
c = 72.2γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2016-10-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54182

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.1401000.06517.47.423705
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.299.91.251.87.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.13822516118599.950.175090.172840.2192RANDOM61.757
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]
0.090.09-0.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.505
r_dihedral_angle_4_deg21.093
r_dihedral_angle_3_deg15.221
r_dihedral_angle_1_deg6.806
r_long_range_B_refined6.596
r_long_range_B_other6.575
r_scangle_other3.519
r_mcangle_it2.425
r_mcangle_other2.424
r_scbond_it2.121
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.505
r_dihedral_angle_4_deg21.093
r_dihedral_angle_3_deg15.221
r_dihedral_angle_1_deg6.806
r_long_range_B_refined6.596
r_long_range_B_other6.575
r_scangle_other3.519
r_mcangle_it2.425
r_mcangle_other2.424
r_scbond_it2.121
r_scbond_other2.121
r_angle_refined_deg1.75
r_mcbond_other1.513
r_mcbond_it1.512
r_angle_other_deg0.981
r_chiral_restr0.101
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2594
Nucleic Acid Atoms
Solvent Atoms142
Heterogen Atoms118

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing