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Structure of Aminopeptidase N from E. coli Suggests a Compartmentalized, Gated Active Site
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 1.8 M Sodium Malonate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.52 65.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.438 α = 90 b = 120.438 β = 90 c = 170.561 γ = 120
Symmetry Space Group P 31 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 2005-11-14 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 0.9797, 0.9798, 0.9612 ALS 8.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.65 20 95.5 0.52 14.1 164250 164250
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.68 89.2 0.5 2 2.8 7598
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 MAD THROUGHOUT 1.65 19.94 164250 141768 4334 85.21 0.1785 0.15781 0.1571 0.1567 0.18062 0.18 RANDOM 16.04
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] -0.07 -0.03 -0.07 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.942 r_dihedral_angle_4_deg 17.604 r_dihedral_angle_3_deg 12.532 r_dihedral_angle_1_deg 5.483 r_sphericity_free 3.579 r_scangle_it 3.025 r_sphericity_bonded 2.574 r_scbond_it 1.927 r_mcangle_it 1.201 r_angle_refined_deg 1.171
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.942 r_dihedral_angle_4_deg 17.604 r_dihedral_angle_3_deg 12.532 r_dihedral_angle_1_deg 5.483 r_sphericity_free 3.579 r_scangle_it 3.025 r_sphericity_bonded 2.574 r_scbond_it 1.927 r_mcangle_it 1.201 r_angle_refined_deg 1.171 r_rigid_bond_restr 1.098 r_mcbond_it 0.779 r_nbtor_refined 0.302 r_nbd_refined 0.197 r_symmetry_vdw_refined 0.182 r_symmetry_hbond_refined 0.179 r_xyhbond_nbd_refined 0.151 r_chiral_restr 0.082 r_metal_ion_refined 0.037 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6940 Nucleic Acid Atoms Solvent Atoms 1162 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling SHELXS phasing