3B3V

Crystal structure of the S228A mutant of the aminopeptidase from Vibrio proteolyticus


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
2.550.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.317α = 90
b = 109.317β = 90
c = 91.003γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray 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
11.2221.729223492234

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 1AMP1.2221.7292234463797.30.150.1490.171RANDOM15.041
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]
-0.1-0.05-0.10.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.866
r_dihedral_angle_4_deg19.001
r_sphericity_free13.922
r_dihedral_angle_3_deg11.825
r_sphericity_bonded7.834
r_dihedral_angle_1_deg6.371
r_scangle_it4.996
r_scbond_it3.599
r_mcangle_it2.58
r_mcbond_it1.819
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.866
r_dihedral_angle_4_deg19.001
r_sphericity_free13.922
r_dihedral_angle_3_deg11.825
r_sphericity_bonded7.834
r_dihedral_angle_1_deg6.371
r_scangle_it4.996
r_scbond_it3.599
r_mcangle_it2.58
r_mcbond_it1.819
r_rigid_bond_restr1.746
r_angle_refined_deg1.67
r_mcbond_other1.24
r_angle_other_deg1.019
r_symmetry_vdw_other0.324
r_symmetry_vdw_refined0.297
r_nbd_refined0.259
r_xyhbond_nbd_refined0.228
r_symmetry_hbond_refined0.227
r_nbd_other0.209
r_nbtor_refined0.181
r_chiral_restr0.105
r_nbtor_other0.089
r_metal_ion_refined0.034
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_gen_planes_other0.003
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2382
Nucleic Acid Atoms
Solvent Atoms218
Heterogen Atoms19

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPphasing