3B35

Crystal structure of the M180A 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
2.4950.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.148α = 90
b = 109.148β = 90
c = 90.99γ = 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)R Merge I (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
11.1410.05912206514.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.12

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 1AMP1.141122065614595.040.150.1490.166RANDOM14.646
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]
-0.01-0.01-0.010.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.163
r_dihedral_angle_4_deg18.861
r_dihedral_angle_3_deg11.358
r_sphericity_free8.116
r_dihedral_angle_1_deg6.317
r_sphericity_bonded4.131
r_scangle_it3.425
r_scbond_it2.516
r_mcangle_it1.892
r_angle_refined_deg1.533
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.163
r_dihedral_angle_4_deg18.861
r_dihedral_angle_3_deg11.358
r_sphericity_free8.116
r_dihedral_angle_1_deg6.317
r_sphericity_bonded4.131
r_scangle_it3.425
r_scbond_it2.516
r_mcangle_it1.892
r_angle_refined_deg1.533
r_rigid_bond_restr1.44
r_mcbond_it1.313
r_symmetry_vdw_refined0.31
r_nbtor_refined0.306
r_nbd_refined0.285
r_symmetry_hbond_refined0.256
r_xyhbond_nbd_refined0.227
r_chiral_restr0.101
r_metal_ion_refined0.077
r_bond_refined_d0.012
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2522
Nucleic Acid Atoms
Solvent Atoms360
Heterogen Atoms15

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing