5YID

Crystal Structure of KNI-10395 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
2.8656.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.6α = 90
b = 107.6β = 90
c = 72.56γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2016-05-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.95372ESRFBM14

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
12.14099.80.06314.4524239
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)
12.12.21001.091.65

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 REPLACEMENTTHROUGHOUT2.13823026121299.790.190050.188260.22498RANDOM65.6
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]
1.441.44-2.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.831
r_dihedral_angle_4_deg17.649
r_dihedral_angle_3_deg16.735
r_dihedral_angle_1_deg7.014
r_long_range_B_refined6.417
r_long_range_B_other6.348
r_scangle_other2.517
r_mcangle_it1.811
r_mcangle_other1.81
r_angle_refined_deg1.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.831
r_dihedral_angle_4_deg17.649
r_dihedral_angle_3_deg16.735
r_dihedral_angle_1_deg7.014
r_long_range_B_refined6.417
r_long_range_B_other6.348
r_scangle_other2.517
r_mcangle_it1.811
r_mcangle_other1.81
r_angle_refined_deg1.61
r_scbond_it1.474
r_scbond_other1.474
r_mcbond_other1.094
r_mcbond_it1.093
r_angle_other_deg0.969
r_chiral_restr0.092
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.002
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 Atoms2594
Nucleic Acid Atoms
Solvent Atoms113
Heterogen Atoms92

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing