5Z65 | pdb_00005z65

Crystal structure of porcine aminopeptidase N ectodomain in functional form


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.2298100 mM Hepes pH 7.2, 0.2 M sodium fluoride, 25% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
3.0960.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 260.327α = 90
b = 62.31β = 100.06
c = 80.569γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2017-05-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNFPSS BEAMLINE BL19U10.979NFPSSBL19U1

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
12.6573.4499.67.73.337252
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.652.7

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4HOM2.6573.4435457175899.490.198320.195580.20.251410.24RANDOM71.826
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]
-1.361.461.59-0.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.065
r_dihedral_angle_4_deg17.545
r_dihedral_angle_3_deg16.646
r_long_range_B_other10.865
r_long_range_B_refined10.864
r_scangle_other8.53
r_dihedral_angle_1_deg7.387
r_mcangle_it7.276
r_mcangle_other7.276
r_scbond_it5.444
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.065
r_dihedral_angle_4_deg17.545
r_dihedral_angle_3_deg16.646
r_long_range_B_other10.865
r_long_range_B_refined10.864
r_scangle_other8.53
r_dihedral_angle_1_deg7.387
r_mcangle_it7.276
r_mcangle_other7.276
r_scbond_it5.444
r_scbond_other5.444
r_mcbond_it4.825
r_mcbond_other4.824
r_angle_refined_deg1.694
r_angle_other_deg1.022
r_chiral_restr0.091
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7228
Nucleic Acid Atoms
Solvent Atoms35
Heterogen Atoms267

Software

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