3EBG

Structure of the M1 Alanylaminopeptidase from malaria


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529822% (v/v) PEG 8000, 10% (v/v) glycerol, 0.1 M Tris (pH 8.5), 0.2 M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3547.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.656α = 90
b = 108.684β = 90
c = 118.399γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVOSMIC MIRRORS2007-10-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEELLIOTT GX-13

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
12.134.695.50.0712.753946
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.2182.30.342.32.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.134.653946286398.510.172790.170260.22034RANDOM17.832
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]
-0.22-0.560.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.231
r_dihedral_angle_4_deg17.183
r_dihedral_angle_3_deg13.414
r_dihedral_angle_1_deg5.775
r_scangle_it2.052
r_scbond_it1.306
r_angle_refined_deg1.134
r_mcangle_it0.791
r_mcbond_it0.488
r_nbtor_refined0.298
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.231
r_dihedral_angle_4_deg17.183
r_dihedral_angle_3_deg13.414
r_dihedral_angle_1_deg5.775
r_scangle_it2.052
r_scbond_it1.306
r_angle_refined_deg1.134
r_mcangle_it0.791
r_mcbond_it0.488
r_nbtor_refined0.298
r_nbd_refined0.185
r_symmetry_vdw_refined0.154
r_xyhbond_nbd_refined0.132
r_symmetry_hbond_refined0.13
r_chiral_restr0.079
r_metal_ion_refined0.07
r_bond_refined_d0.01
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
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 Atoms7177
Nucleic Acid Atoms
Solvent Atoms762
Heterogen Atoms33

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection