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Crystal structure of porcine aminopeptidase-N with Isoleucine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FKE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.2 277 18% PEG3350, 200 MM LITHIUM SULFATE,
100 MM HEPES
Crystal Properties Matthews coefficient Solvent content 3.21 61.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 260.359 α = 90 b = 62.923 β = 100.51 c = 81.733 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 100 CCD ADSC QUANTUM 315 2012-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 1 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.15 50 99 0.116 16.29 6.5 69735
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.23 92.6 0.572 2.33 4.4 6475
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 4FKE 2.14 50 66189 3512 97.04 0.2155 0.21322 0.2166 0.25744 0.2596 RANDOM 37.142
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] -0.73 0.59 0.86 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.378 r_dihedral_angle_4_deg 20.688 r_dihedral_angle_3_deg 16.619 r_sphericity_free 8.148 r_dihedral_angle_1_deg 7.522 r_rigid_bond_restr 4.885 r_sphericity_bonded 3.423 r_long_range_B_refined 2.069 r_long_range_B_other 2.02 r_angle_other_deg 2.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.378 r_dihedral_angle_4_deg 20.688 r_dihedral_angle_3_deg 16.619 r_sphericity_free 8.148 r_dihedral_angle_1_deg 7.522 r_rigid_bond_restr 4.885 r_sphericity_bonded 3.423 r_long_range_B_refined 2.069 r_long_range_B_other 2.02 r_angle_other_deg 2.01 r_mcangle_it 1.903 r_mcangle_other 1.903 r_scangle_other 1.667 r_angle_refined_deg 1.626 r_mcbond_it 1.619 r_mcbond_other 1.619 r_scbond_it 1.567 r_scbond_other 1.516 r_chiral_restr 0.116 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_gen_planes_other 0.006 r_bond_other_d 0.002 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7242 Nucleic Acid Atoms Solvent Atoms 657 Heterogen Atoms 382
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing