6R4Y

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.151.5 microl 12 mg per ml rPPEP-1 E143A Y178F with 6 mM substrate peptide (Ac-EVNPAVP-CONH2) in 20 mM Tris pH 7.5, 200 mM NaCl, 0.1 mM ZnCl2 was mixed with 1.5 microl precipitant solution containing: 100 mM Tris pH 8.5, 2.1 M ammonium phosphate dibasic. Reservoir volume: 200 microl
Crystal Properties
Matthews coefficientSolvent content
2.0941.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.036α = 90
b = 42.8β = 92.78
c = 118.274γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80PIXELDECTRIS PILATUS 2M-F2016-12-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1SLSX06DA

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
11.45240.2498.1816.625.664508
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.4521.504

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-VALUE5A0P1.45240.241.4264508200198.150.14570.14510.1652
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_d13.109
f_angle_d0.896
f_chiral_restr0.071
f_bond_d0.007
f_plane_restr0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3083
Nucleic Acid Atoms
Solvent Atoms376
Heterogen Atoms2

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing