7VE2

Crystal Structure of Lopinavir bound Plasmepsin II (PMII) from Plasmodium falciparum


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5YIC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52931.4 M ammonium sulfate, 0.1 M Bis-Tris pH 5.5
Crystal Properties
Matthews coefficientSolvent content
2.8156.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.94α = 90
b = 108.94β = 90
c = 70.2γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2020-03-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
13.238.5299.90.999.957.54687787.22
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.23.31000.371.047.57

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT5YIC3.238.52653134499.850.22680.224590.26617RANDOM127.423
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]
5.265.26-10.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.217
r_dihedral_angle_3_deg20.908
r_dihedral_angle_4_deg12.205
r_dihedral_angle_1_deg9.262
r_long_range_B_other6.985
r_long_range_B_refined6.984
r_scangle_other2.724
r_mcangle_it2.423
r_mcangle_other2.423
r_scbond_it1.526
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.217
r_dihedral_angle_3_deg20.908
r_dihedral_angle_4_deg12.205
r_dihedral_angle_1_deg9.262
r_long_range_B_other6.985
r_long_range_B_refined6.984
r_scangle_other2.724
r_mcangle_it2.423
r_mcangle_other2.423
r_scbond_it1.526
r_scbond_other1.522
r_angle_refined_deg1.437
r_mcbond_it1.37
r_mcbond_other1.37
r_angle_other_deg1.1
r_chiral_restr0.057
r_gen_planes_refined0.005
r_bond_refined_d0.004
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 Atoms2606
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms130

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing