4K5L

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 3EBGpdb entry 3EBG

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
2.3647.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.094α = 90
b = 109.345β = 90
c = 118.706γ = 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
11.9180.4299.71100704773262
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.912.0197.7

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 3EBG1.9180.4273397392399.590.173960.17150.21982RANDOM22.267
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]
-0.55-0.781.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.088
r_dihedral_angle_4_deg18.172
r_dihedral_angle_3_deg14.271
r_dihedral_angle_1_deg6.2
r_scangle_it4.752
r_scbond_it3.109
r_angle_refined_deg1.774
r_mcangle_it1.774
r_mcbond_it1.074
r_chiral_restr0.146
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.088
r_dihedral_angle_4_deg18.172
r_dihedral_angle_3_deg14.271
r_dihedral_angle_1_deg6.2
r_scangle_it4.752
r_scbond_it3.109
r_angle_refined_deg1.774
r_mcangle_it1.774
r_mcbond_it1.074
r_chiral_restr0.146
r_bond_refined_d0.023
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7219
Nucleic Acid Atoms
Solvent Atoms544
Heterogen Atoms16

Software

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