6BV0

Crystal structure of porcine aminopeptidase-N with Arginine


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
3.261.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 260.646α = 90
b = 62.865β = 100.57
c = 81.721γ = 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
11.865098.20.07518.574.3107699
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)
11.861.9384.40.4841.892.49180

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 REPLACEMENTTHROUGHOUT4FKE1.8650102042536897.940.217250.214970.26029RANDOM32.463
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]
-0.241.21-0.340.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.781
r_dihedral_angle_4_deg17.453
r_dihedral_angle_3_deg16.006
r_dihedral_angle_1_deg7.27
r_rigid_bond_restr6.563
r_sphericity_free5.283
r_sphericity_bonded3.118
r_angle_other_deg1.957
r_long_range_B_refined1.87
r_long_range_B_other1.841
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.781
r_dihedral_angle_4_deg17.453
r_dihedral_angle_3_deg16.006
r_dihedral_angle_1_deg7.27
r_rigid_bond_restr6.563
r_sphericity_free5.283
r_sphericity_bonded3.118
r_angle_other_deg1.957
r_long_range_B_refined1.87
r_long_range_B_other1.841
r_mcangle_it1.766
r_mcangle_other1.766
r_mcbond_it1.705
r_mcbond_other1.704
r_scbond_it1.587
r_scbond_other1.564
r_scangle_other1.53
r_angle_refined_deg1.18
r_chiral_restr0.094
r_bond_refined_d0.012
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 Atoms7241
Nucleic Acid Atoms
Solvent Atoms859
Heterogen Atoms385

Software

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