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Crystal structure of porcine aminopeptidase N complexed with CNGRCG tumor-homing peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FKE PDB ENTRY 4FKE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.2 277 2 uL protein + 2 uL well solution (18% v/v PEG3350, 200 mM lithium sulfate, 100 mM HEPES, pH 7.2), VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.17 61.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 260.323 α = 90 b = 62.879 β = 100.59 c = 82.023 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD NOIR-1 2013-01-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 ALS 4.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 1.92 50 97.9 0.079 0.079 20.7 3.8 95642
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.92 1.96 97 0.615 0.615 1.7 3.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 4FKE 1.95 50 88648 4699 97.85 0.14285 0.14038 0.1441 0.18956 0.1876 RANDOM 49.799
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] -0.59 -0.35 0.35 0.35
RMS Deviations Key Refinement Restraint Deviation r_sphericity_bonded 43.043 r_dihedral_angle_2_deg 40.055 r_sphericity_free 22.47 r_dihedral_angle_4_deg 16.523 r_dihedral_angle_3_deg 14.424 r_long_range_B_refined 10.931 r_scbond_it 10.842 r_mcangle_it 6.611 r_dihedral_angle_1_deg 6.328 r_mcbond_it 5.551
RMS Deviations Key Refinement Restraint Deviation r_sphericity_bonded 43.043 r_dihedral_angle_2_deg 40.055 r_sphericity_free 22.47 r_dihedral_angle_4_deg 16.523 r_dihedral_angle_3_deg 14.424 r_long_range_B_refined 10.931 r_scbond_it 10.842 r_mcangle_it 6.611 r_dihedral_angle_1_deg 6.328 r_mcbond_it 5.551 r_rigid_bond_restr 3.225 r_angle_refined_deg 1.614 r_chiral_restr 0.098 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7281 Nucleic Acid Atoms Solvent Atoms 906 Heterogen Atoms 303
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling CCP4 phasing