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Crystal structure of porcine aminopeptidase N ectodomain in functional form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HOM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.2 298 100 mM Hepes pH 7.2, 0.2 M sodium fluoride, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.09 60.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 260.327 α = 90 b = 62.31 β = 100.06 c = 80.569 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 PIXEL DECTRIS PILATUS3 S 6M 2017-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NFPSS BEAMLINE BL19U1 0.979 NFPSS BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.65 73.44 99.6 7.7 3.3 37252
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.65 2.7
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 4HOM 2.65 73.44 35457 1758 99.49 0.19832 0.19558 0.2011 0.25141 0.2412 RANDOM 71.826
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] -1.36 1.46 1.59 -0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.065 r_dihedral_angle_4_deg 17.545 r_dihedral_angle_3_deg 16.646 r_long_range_B_other 10.865 r_long_range_B_refined 10.864 r_scangle_other 8.53 r_dihedral_angle_1_deg 7.387 r_mcangle_it 7.276 r_mcangle_other 7.276 r_scbond_it 5.444
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.065 r_dihedral_angle_4_deg 17.545 r_dihedral_angle_3_deg 16.646 r_long_range_B_other 10.865 r_long_range_B_refined 10.864 r_scangle_other 8.53 r_dihedral_angle_1_deg 7.387 r_mcangle_it 7.276 r_mcangle_other 7.276 r_scbond_it 5.444 r_scbond_other 5.444 r_mcbond_it 4.825 r_mcbond_other 4.824 r_angle_refined_deg 1.694 r_angle_other_deg 1.022 r_chiral_restr 0.091 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7228 Nucleic Acid Atoms Solvent Atoms 35 Heterogen Atoms 267
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing