3B7I

Crystal structure of the S228A mutant of the aminopeptidase from Vibrio proteolyticus in complex with leucine phosphonic acid


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, NaCl, KSCN, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.5351.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.907α = 90
b = 109.907β = 90
c = 91.095γ = 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
11.7520.373278932789

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 1AMP1.7520.3732789165598.740.1780.1770.209RANDOM14.089
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]
0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.933
r_dihedral_angle_4_deg20.195
r_dihedral_angle_3_deg12.138
r_dihedral_angle_1_deg5.856
r_scangle_it3.23
r_scbond_it2.071
r_angle_refined_deg1.283
r_mcangle_it1.185
r_mcbond_it0.675
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.933
r_dihedral_angle_4_deg20.195
r_dihedral_angle_3_deg12.138
r_dihedral_angle_1_deg5.856
r_scangle_it3.23
r_scbond_it2.071
r_angle_refined_deg1.283
r_mcangle_it1.185
r_mcbond_it0.675
r_nbtor_refined0.303
r_symmetry_vdw_refined0.224
r_nbd_refined0.216
r_metal_ion_refined0.216
r_symmetry_hbond_refined0.143
r_xyhbond_nbd_refined0.136
r_symmetry_metal_ion_refined0.127
r_chiral_restr0.088
r_bond_refined_d0.012
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2263
Nucleic Acid Atoms
Solvent Atoms250
Heterogen Atoms8

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPphasing