3B3W

Crystal structure of the S228A 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
2.5752.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.549α = 90
b = 110.549β = 90
c = 91.626γ = 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
11.7514.983065430654

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 1AMP1.7514.9830654157490.690.1960.1940.234RANDOM27.352
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]
-0.01-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.679
r_dihedral_angle_4_deg23.2
r_dihedral_angle_3_deg13.99
r_dihedral_angle_1_deg6.27
r_scangle_it3.492
r_scbond_it2.269
r_angle_refined_deg1.463
r_mcangle_it1.445
r_mcbond_it0.838
r_symmetry_metal_ion_refined0.612
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.679
r_dihedral_angle_4_deg23.2
r_dihedral_angle_3_deg13.99
r_dihedral_angle_1_deg6.27
r_scangle_it3.492
r_scbond_it2.269
r_angle_refined_deg1.463
r_mcangle_it1.445
r_mcbond_it0.838
r_symmetry_metal_ion_refined0.612
r_symmetry_hbond_refined0.39
r_nbtor_refined0.306
r_symmetry_vdw_refined0.275
r_nbd_refined0.217
r_metal_ion_refined0.191
r_xyhbond_nbd_refined0.154
r_chiral_restr0.099
r_bond_refined_d0.014
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2213
Nucleic Acid Atoms
Solvent Atoms261
Heterogen Atoms16

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPphasing