4K5M

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 3EBHpdb entry 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
2.3447.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.995α = 90
b = 109.035β = 90
c = 118.576γ = 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
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX10.95467Australian SynchrotronMX1

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
11.7580.3298.91433526992592
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.8492.2

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 REPLACEMENTTHROUGHOUTpdb entry 3ebh1.7580.2694217495298.840.164770.162540.206573EBH19.44
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]
-0.850.85
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.256
r_dihedral_angle_4_deg21.423
r_dihedral_angle_3_deg13.623
r_dihedral_angle_1_deg6.083
r_scangle_it5.09
r_scbond_it3.251
r_mcangle_it1.981
r_angle_refined_deg1.915
r_mcbond_it1.2
r_chiral_restr0.159
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.256
r_dihedral_angle_4_deg21.423
r_dihedral_angle_3_deg13.623
r_dihedral_angle_1_deg6.083
r_scangle_it5.09
r_scbond_it3.251
r_mcangle_it1.981
r_angle_refined_deg1.915
r_mcbond_it1.2
r_chiral_restr0.159
r_bond_refined_d0.025
r_gen_planes_refined0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7208
Nucleic Acid Atoms
Solvent Atoms1147
Heterogen Atoms34

Software

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