3B3S

Crystal structure of the M180A mutant of the aminopeptidase from Vibrio proteolyticus in complex with leucine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1AMPPDB entry 1AMP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8298HEPES, KSCN, NaCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.5151

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.485α = 90
b = 109.485β = 90
c = 91.022γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-C0.90010APS14-BM-C

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
11.1817.21102599102599

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1AMP1.1817.21102599513997.760.1680.1680.1660.196RANDOM15.454
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]
-0.03-0.01-0.030.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.633
r_dihedral_angle_4_deg18.838
r_dihedral_angle_3_deg11.304
r_sphericity_free7.965
r_dihedral_angle_1_deg5.95
r_sphericity_bonded5.446
r_scangle_it4.433
r_scbond_it3.228
r_mcangle_it2.528
r_mcbond_it1.776
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.633
r_dihedral_angle_4_deg18.838
r_dihedral_angle_3_deg11.304
r_sphericity_free7.965
r_dihedral_angle_1_deg5.95
r_sphericity_bonded5.446
r_scangle_it4.433
r_scbond_it3.228
r_mcangle_it2.528
r_mcbond_it1.776
r_rigid_bond_restr1.715
r_angle_refined_deg1.618
r_symmetry_hbond_refined0.436
r_nbtor_refined0.313
r_symmetry_vdw_refined0.311
r_nbd_refined0.235
r_metal_ion_refined0.177
r_xyhbond_nbd_refined0.175
r_symmetry_metal_ion_refined0.17
r_chiral_restr0.102
r_bond_refined_d0.015
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2355
Nucleic Acid Atoms
Solvent Atoms299
Heterogen Atoms25

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction