6BV2

Crystal structure of porcine aminopeptidase-N with Isoleucine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4FKE 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.227718% PEG3350, 200 MM LITHIUM SULFATE, 100 MM HEPES
Crystal Properties
Matthews coefficientSolvent content
3.2161.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 260.359α = 90
b = 62.923β = 100.51
c = 81.733γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152012-06-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-E1APS24-ID-E

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.1550990.11616.296.569735
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.152.2392.60.5722.334.46475

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 REPLACEMENTTHROUGHOUT4FKE2.145066189351297.040.21550.213220.25744RANDOM37.142
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]
-0.730.590.86-0.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.378
r_dihedral_angle_4_deg20.688
r_dihedral_angle_3_deg16.619
r_sphericity_free8.148
r_dihedral_angle_1_deg7.522
r_rigid_bond_restr4.885
r_sphericity_bonded3.423
r_long_range_B_refined2.069
r_long_range_B_other2.02
r_angle_other_deg2.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.378
r_dihedral_angle_4_deg20.688
r_dihedral_angle_3_deg16.619
r_sphericity_free8.148
r_dihedral_angle_1_deg7.522
r_rigid_bond_restr4.885
r_sphericity_bonded3.423
r_long_range_B_refined2.069
r_long_range_B_other2.02
r_angle_other_deg2.01
r_mcangle_it1.903
r_mcangle_other1.903
r_scangle_other1.667
r_angle_refined_deg1.626
r_mcbond_it1.619
r_mcbond_other1.619
r_scbond_it1.567
r_scbond_other1.516
r_chiral_restr0.116
r_bond_refined_d0.019
r_gen_planes_refined0.009
r_gen_planes_other0.006
r_bond_other_d0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7242
Nucleic Acid Atoms
Solvent Atoms657
Heterogen Atoms382

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing