6BV3

Crystal structure of porcine aminopeptidase-N with Leucine


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
3.261.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 259.55α = 90
b = 62.985β = 100.38
c = 81.647γ = 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
12.25099.10.09222.787.165231
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)
12.22.2895.70.6012.634.86262

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 REPLACEMENTTHROUGHOUT4FKE2.25061854330998.850.214720.211680.26986RANDOM36.228
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]
0.090.59-0.440.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.171
r_dihedral_angle_3_deg17.607
r_dihedral_angle_4_deg17.606
r_sphericity_free8.2
r_dihedral_angle_1_deg7.767
r_rigid_bond_restr4.576
r_sphericity_bonded3.468
r_angle_other_deg1.997
r_long_range_B_refined1.958
r_long_range_B_other1.881
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.171
r_dihedral_angle_3_deg17.607
r_dihedral_angle_4_deg17.606
r_sphericity_free8.2
r_dihedral_angle_1_deg7.767
r_rigid_bond_restr4.576
r_sphericity_bonded3.468
r_angle_other_deg1.997
r_long_range_B_refined1.958
r_long_range_B_other1.881
r_mcangle_it1.764
r_mcangle_other1.763
r_scangle_other1.545
r_mcbond_it1.46
r_mcbond_other1.46
r_scbond_it1.46
r_angle_refined_deg1.441
r_scbond_other1.389
r_chiral_restr0.108
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_gen_planes_other0.005
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 Atoms748
Heterogen Atoms387

Software

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