4K5O

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, vapor diffusion, hanging drop, temperature 298K, pH 8.5, VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.3647.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.056α = 90
b = 109.35β = 90
c = 118.518γ = 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)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
11.980.3796.40.144111369375260

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 DIFFRACTIONTHROUGHOUT3EBH1.964.0174673380195.610.18470.18160.2407RANDOM20.831
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]
0.11-0.680.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.547
r_dihedral_angle_4_deg18.997
r_dihedral_angle_3_deg14.533
r_dihedral_angle_1_deg6.336
r_scangle_it4.877
r_scbond_it3.284
r_angle_refined_deg1.89
r_mcangle_it1.887
r_mcbond_it1.148
r_chiral_restr0.142
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.547
r_dihedral_angle_4_deg18.997
r_dihedral_angle_3_deg14.533
r_dihedral_angle_1_deg6.336
r_scangle_it4.877
r_scbond_it3.284
r_angle_refined_deg1.89
r_mcangle_it1.887
r_mcbond_it1.148
r_chiral_restr0.142
r_bond_refined_d0.024
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7200
Nucleic Acid Atoms
Solvent Atoms1014
Heterogen Atoms32

Software

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