6BUY

Crystal structure of porcine aminopeptidase-N with Glycine


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
3.261.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 260.606α = 90
b = 62.733β = 100.26
c = 81.636γ = 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
12.15099.90.06120.113.772167
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)
12.12.1899.80.4643.133.8

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 REPLACEMENTTHROUGHOUT4FKE2.1128.2272167381799.790.199170.196550.24804RANDOM32.088
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]
0.150.740.09-0.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.679
r_dihedral_angle_4_deg19.714
r_dihedral_angle_3_deg16.069
r_dihedral_angle_1_deg7.037
r_sphericity_free6.729
r_rigid_bond_restr5.706
r_sphericity_bonded3.233
r_angle_other_deg2.01
r_long_range_B_refined1.848
r_long_range_B_other1.787
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.679
r_dihedral_angle_4_deg19.714
r_dihedral_angle_3_deg16.069
r_dihedral_angle_1_deg7.037
r_sphericity_free6.729
r_rigid_bond_restr5.706
r_sphericity_bonded3.233
r_angle_other_deg2.01
r_long_range_B_refined1.848
r_long_range_B_other1.787
r_mcangle_it1.688
r_mcangle_other1.688
r_angle_refined_deg1.628
r_scangle_other1.534
r_mcbond_it1.488
r_mcbond_other1.488
r_scbond_it1.462
r_scbond_other1.42
r_chiral_restr0.122
r_bond_refined_d0.021
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 Atoms932
Heterogen Atoms378

Software

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