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Crystal structure of porcine aminopeptidase-N with Methionine
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 3.2 61.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 260.664 α = 90 b = 62.871 β = 100.39 c = 81.62 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 2.03 50 98.9 0.085 21.43 7.4 84218
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 2.03 2.1 90 0.425 3.62 5.5
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 2.02 50 79921 4211 98.59 0.20716 0.20512 0.2108 0.24571 0.253 RANDOM 32.415
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] -0.09 0.91 -0.27 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.072 r_dihedral_angle_4_deg 19.593 r_dihedral_angle_3_deg 16.538 r_dihedral_angle_1_deg 7.392 r_rigid_bond_restr 6.407 r_sphericity_free 6.355 r_sphericity_bonded 3.299 r_angle_other_deg 1.959 r_long_range_B_refined 1.947 r_long_range_B_other 1.909
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.072 r_dihedral_angle_4_deg 19.593 r_dihedral_angle_3_deg 16.538 r_dihedral_angle_1_deg 7.392 r_rigid_bond_restr 6.407 r_sphericity_free 6.355 r_sphericity_bonded 3.299 r_angle_other_deg 1.959 r_long_range_B_refined 1.947 r_long_range_B_other 1.909 r_mcangle_other 1.822 r_mcangle_it 1.821 r_mcbond_it 1.7 r_mcbond_other 1.699 r_scangle_other 1.648 r_scbond_it 1.634 r_scbond_other 1.586 r_angle_refined_deg 1.166 r_chiral_restr 0.094 r_bond_refined_d 0.012 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 839 Heterogen Atoms 392
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing