4HOM

Crystal structure of porcine aminopeptidase-N complexed with substance P


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.227718% PEG3350, 200 mM lithium sulfate, 100 mM HEPES, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.1360.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 261.573α = 90
b = 62.598β = 100.27
c = 81.553γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDADSC QUANTUM 315MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-IDAPS19-ID

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
11.855098.210261810077422

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.937.1895596502798.050.149790.14710.20123RANDOM33.54
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]
0.830.86-0.29-0.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.118
r_sphericity_free26.212
r_sphericity_bonded16.98
r_dihedral_angle_4_deg16.012
r_dihedral_angle_3_deg14.42
r_dihedral_angle_1_deg6.36
r_rigid_bond_restr2.169
r_angle_refined_deg1.127
r_chiral_restr0.08
r_bond_refined_d0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.118
r_sphericity_free26.212
r_sphericity_bonded16.98
r_dihedral_angle_4_deg16.012
r_dihedral_angle_3_deg14.42
r_dihedral_angle_1_deg6.36
r_rigid_bond_restr2.169
r_angle_refined_deg1.127
r_chiral_restr0.08
r_bond_refined_d0.006
r_gen_planes_refined0.005
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_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7336
Nucleic Acid Atoms
Solvent Atoms1434
Heterogen Atoms323

Software

Software
Software NamePurpose
HKL-2000data collection
SOLVEphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling