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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
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5AB0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277.15 10% 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 coefficient Solvent content 2.92 57.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.135 α = 90 b = 133.822 β = 90.285 c = 128.703 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2019-08-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9763 PETRA III, EMBL c/o DESY P13 (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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.7 65.03 88.6 0.0441 0.0441 0.998 10.76 2 61923 65.41
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.797 0.68 1.72
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5AB0 2.7 65.03 1.36 61917 3101 88.6 0.1908 0.1882 0.1901 0.2384 0.2389
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 Key Refinement Restraint Deviation f_dihedral_angle_d 6.142 f_angle_d 1.408 f_chiral_restr 0.0787 f_bond_d 0.0115 f_plane_restr 0.0082
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14145 Nucleic Acid Atoms Solvent Atoms 80 Heterogen Atoms 537
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction XDS data scaling PHASER phasing