6R4Z

Crystal structure of holo PPEP-1(E143A/Y178F) in complex with product peptide Ac-EVNP-CO2 (substrate peptide: Ac-EVNPPVP-CONH2)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5A0P 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.151 microl 12 mg per ml rPPEP-1 E143A Y178F with 6 mM substrate peptide (Ac-EVNPPVP-CONH2) in 20 mM Tris pH 7.5, 200 mM NaCl, 0.1 mM ZnCl2 was mixed with 2 microL precipitant solution containing: 100 mM Tris pH 8.5, 2.55 M ammonium phosphate dibasic. Reservoir volume: 200 microl
Crystal Properties
Matthews coefficientSolvent content
2.1141.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.039α = 90
b = 42.806β = 92.41
c = 119.048γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80PIXELDECTRIS EIGER X 16M2016-06-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA0.73SLSX06SA

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
11.05234.92298.6822.226.81163245170479
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.0521.09

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5A0P1.05234.9221.5170477200498.60.1330.13280.1513
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d12.384
f_angle_d1.006
f_chiral_restr0.077
f_bond_d0.009
f_plane_restr0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3119
Nucleic Acid Atoms
Solvent Atoms631
Heterogen Atoms3

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing