4K5P

Phosphonic Arginine Mimetics as Inhibitors of the M1 Aminopeptidases from Plasmodium falciparum


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3EBH 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529822% (v/v) PEG 8000, 10% (v/v) glycerol, 0.1 M Tris, 0.2 M MgCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3547.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.794α = 90
b = 109.048β = 90
c = 118.84γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2010-02-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.95467DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.8580.35100125829884723

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 REPLACEMENTTHROUGHOUT3EBH1.8580.358464042921000.17480.17210.22463EBH23.0722
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]
-0.57-0.431
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.928
r_dihedral_angle_4_deg22.906
r_dihedral_angle_3_deg14.712
r_dihedral_angle_1_deg6.142
r_scangle_it5.231
r_scbond_it3.383
r_mcangle_it1.978
r_angle_refined_deg1.855
r_mcbond_it1.171
r_chiral_restr0.137
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.928
r_dihedral_angle_4_deg22.906
r_dihedral_angle_3_deg14.712
r_dihedral_angle_1_deg6.142
r_scangle_it5.231
r_scbond_it3.383
r_mcangle_it1.978
r_angle_refined_deg1.855
r_mcbond_it1.171
r_chiral_restr0.137
r_bond_refined_d0.023
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7276
Nucleic Acid Atoms
Solvent Atoms978
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
XDSdata reduction
SCALAdata scaling
PHASERphasing