3EBH

Structure of the M1 Alanylaminopeptidase from malaria complexed with bestatin


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1vapor diffusion, hanging dro8.529822% (v/v) PEG 8000, 10% (v/v) glycerol, 0.1 M Tris (pH 8.5), 0.2 M MgCl2, vapor diffusion, hanging dro, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3447.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.651α = 90
b = 108.628β = 90
c = 117.964γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2008-03-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX11.0Australian SynchrotronMX1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.6527.5783.20.0640.0648.6732.8120212
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.651.7474.60.3690.3691.82.3

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 REPLACEMENTTHROUGHOUT1.6527.4790285475981.090.17830.177030.20219RANDOM13.32
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]
0.22-0.790.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.314
r_dihedral_angle_4_deg15.766
r_dihedral_angle_3_deg11.808
r_dihedral_angle_1_deg5.303
r_scangle_it3.826
r_scbond_it2.519
r_mcangle_it1.476
r_angle_refined_deg0.973
r_mcbond_it0.901
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.314
r_dihedral_angle_4_deg15.766
r_dihedral_angle_3_deg11.808
r_dihedral_angle_1_deg5.303
r_scangle_it3.826
r_scbond_it2.519
r_mcangle_it1.476
r_angle_refined_deg0.973
r_mcbond_it0.901
r_nbtor_refined0.302
r_nbd_refined0.182
r_symmetry_vdw_refined0.152
r_symmetry_hbond_refined0.136
r_xyhbond_nbd_refined0.085
r_chiral_restr0.069
r_metal_ion_refined0.036
r_bond_refined_d0.006
r_gen_planes_refined0.003
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 Atoms7290
Nucleic Acid Atoms
Solvent Atoms876
Heterogen Atoms63

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction