5YIC

Crystal Structure of KNI-10333 bound Plasmepsin II (PMII) from Plasmodium falciparum


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52950.2 M lithium sulfate, 1.26 M ammonium sulfate, 0.1 M Tris pH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.7354.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.5α = 90
b = 106.5β = 90
c = 71γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2016-04-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.9537ESRFBM14

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
11.94099.70.05616.65.331284
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)
11.9299.71.231.55.2

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 REPLACEMENTTHROUGHOUT1.937.6529718156599.730.180370.177950.22699RANDOM48.159
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]
-0.12-0.120.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.528
r_dihedral_angle_4_deg20.396
r_dihedral_angle_3_deg15.168
r_long_range_B_other7.457
r_long_range_B_refined7.456
r_dihedral_angle_1_deg6.624
r_scangle_other2.882
r_mcangle_it2.062
r_mcangle_other2.062
r_scbond_it1.806
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.528
r_dihedral_angle_4_deg20.396
r_dihedral_angle_3_deg15.168
r_long_range_B_other7.457
r_long_range_B_refined7.456
r_dihedral_angle_1_deg6.624
r_scangle_other2.882
r_mcangle_it2.062
r_mcangle_other2.062
r_scbond_it1.806
r_scbond_other1.805
r_angle_refined_deg1.661
r_mcbond_it1.31
r_mcbond_other1.308
r_angle_other_deg0.968
r_chiral_restr0.103
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d0.003
r_gen_planes_other0.003
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 Atoms2600
Nucleic Acid Atoms
Solvent Atoms251
Heterogen Atoms116

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing