5YIB

Crystal Structure of KNI-10743 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
2.7154.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.25α = 90
b = 106.25β = 90
c = 70.85γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2016-05-19MSINGLE 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
12.154099.90.08716.97.321566
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)
12.152.2599.90.9926.9

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 REPLACEMENTTHROUGHOUT2.153920484107899.940.179020.178090.19644RANDOM50.453
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]
-0.98-0.981.96
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.821
r_dihedral_angle_4_deg24.711
r_dihedral_angle_3_deg15.859
r_dihedral_angle_1_deg6.921
r_long_range_B_refined5.351
r_long_range_B_other5.351
r_scangle_other2.46
r_mcangle_it1.966
r_mcangle_other1.965
r_angle_refined_deg1.529
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.821
r_dihedral_angle_4_deg24.711
r_dihedral_angle_3_deg15.859
r_dihedral_angle_1_deg6.921
r_long_range_B_refined5.351
r_long_range_B_other5.351
r_scangle_other2.46
r_mcangle_it1.966
r_mcangle_other1.965
r_angle_refined_deg1.529
r_scbond_it1.481
r_scbond_other1.48
r_mcbond_it1.159
r_mcbond_other1.159
r_angle_other_deg0.938
r_chiral_restr0.086
r_bond_refined_d0.01
r_bond_other_d0.006
r_gen_planes_refined0.005
r_gen_planes_other0.001
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 Atoms114
Heterogen Atoms121

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing