3B3T

Crystal structure of the D118N 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
2.550.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.294α = 90
b = 109.294β = 90
c = 91.009γ = 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
11.1742102258102258

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 1AMP1.1742102258510195.350.1430.1420.161RANDOM11.391
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]
0.010.010.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.091
r_dihedral_angle_4_deg22.371
r_dihedral_angle_3_deg11.263
r_sphericity_free9.694
r_dihedral_angle_1_deg6.114
r_sphericity_bonded5.079
r_scangle_it4.328
r_scbond_it3.047
r_mcangle_it2.209
r_symmetry_metal_ion_refined1.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.091
r_dihedral_angle_4_deg22.371
r_dihedral_angle_3_deg11.263
r_sphericity_free9.694
r_dihedral_angle_1_deg6.114
r_sphericity_bonded5.079
r_scangle_it4.328
r_scbond_it3.047
r_mcangle_it2.209
r_symmetry_metal_ion_refined1.62
r_angle_refined_deg1.617
r_mcbond_it1.532
r_rigid_bond_restr1.525
r_angle_other_deg0.968
r_mcbond_other0.851
r_symmetry_vdw_refined0.423
r_symmetry_vdw_other0.371
r_nbd_refined0.242
r_nbd_other0.201
r_xyhbond_nbd_refined0.191
r_nbtor_refined0.181
r_symmetry_hbond_refined0.179
r_chiral_restr0.097
r_nbtor_other0.09
r_metal_ion_refined0.05
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_gen_planes_other0.003
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2321
Nucleic Acid Atoms
Solvent Atoms292
Heterogen Atoms20

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction