7PFS

Crystal structure of ERAP2 aminopeptidase in complex with phosphinic pseudotripeptide ((1R)-1-Amino-3-phenylpropyl){2-([1,1:3,1-terphenyl]-5-ylmethyl)-3-[((2S)-1-amino-1-oxo-3-phenylpropan-2-yl)-amino]-3-oxopropyl}phosphinic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5AB0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5277.1510% w/v PEG 8000, 20% v/v ethylene glycol, 0.02M of each monosaccharide (0.2M D-glucose, 0.2M D-mannose, 0.2M D-galactose,0.2M L-fucose, 0.2M D-xylose, 0.2M N-acetyl-D-glucosamine), 0.1M MES/imidazole pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.9257.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.135α = 90
b = 133.822β = 90.285
c = 128.703γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-08-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)0.9763PETRA III, EMBL c/o DESYP13 (MX1)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)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
12.765.0388.60.04410.04410.99810.7626192365.41
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.72.7970.681.72

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-VALUE5AB02.765.031.3661917310188.60.19080.18820.2384
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_d6.142
f_angle_d1.408
f_chiral_restr0.0787
f_bond_d0.0115
f_plane_restr0.0082
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14145
Nucleic Acid Atoms
Solvent Atoms80
Heterogen Atoms537

Software

Software
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing