4OU3

Crystal structure of porcine aminopeptidase N complexed with CNGRCG tumor-homing peptide


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.22772 uL protein + 2 uL well solution (18% v/v PEG3350, 200 mM lithium sulfate, 100 mM HEPES, pH 7.2), VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.1761.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 260.323α = 90
b = 62.879β = 100.59
c = 82.023γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDNOIR-12013-01-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 4.2.2ALS4.2.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.925097.90.0790.07920.73.895642
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.921.96970.6150.6151.73.9

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 4FKE1.955088648469997.850.142850.140380.18956RANDOM49.799
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]
-0.59-0.350.350.35
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_bonded43.043
r_dihedral_angle_2_deg40.055
r_sphericity_free22.47
r_dihedral_angle_4_deg16.523
r_dihedral_angle_3_deg14.424
r_long_range_B_refined10.931
r_scbond_it10.842
r_mcangle_it6.611
r_dihedral_angle_1_deg6.328
r_mcbond_it5.551
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_bonded43.043
r_dihedral_angle_2_deg40.055
r_sphericity_free22.47
r_dihedral_angle_4_deg16.523
r_dihedral_angle_3_deg14.424
r_long_range_B_refined10.931
r_scbond_it10.842
r_mcangle_it6.611
r_dihedral_angle_1_deg6.328
r_mcbond_it5.551
r_rigid_bond_restr3.225
r_angle_refined_deg1.614
r_chiral_restr0.098
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7281
Nucleic Acid Atoms
Solvent Atoms906
Heterogen Atoms303

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing