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Crystal structure of E.coli aminopeptidase N in complex with Puromycin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HPO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 2.0M Sodium malonate
Crystal Properties Matthews coefficient Solvent content 3.51 64.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.292 α = 90 b = 120.292 β = 90 c = 170.123 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 IMAGE PLATE RIGAKU RAXIS IV++ 2016-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.56 50 98.6 0.035 0.039 0.016 0.999 24 4.7 198652 22.44
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.56 1.62 100 0.337 0.381 0.17 0.906 4.37 4.5
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 2HPO 1.56 50 187925 9844 98.16 0.16239 0.16136 0.1754 0.18189 0.1938 RANDOM 23.628
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.053 r_dihedral_angle_4_deg 16.407 r_dihedral_angle_3_deg 12.239 r_long_range_B_refined 6.212 r_long_range_B_other 6.096 r_dihedral_angle_1_deg 6.076 r_scangle_other 5.474 r_scbond_it 3.814 r_scbond_other 3.811 r_angle_refined_deg 2.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.053 r_dihedral_angle_4_deg 16.407 r_dihedral_angle_3_deg 12.239 r_long_range_B_refined 6.212 r_long_range_B_other 6.096 r_dihedral_angle_1_deg 6.076 r_scangle_other 5.474 r_scbond_it 3.814 r_scbond_other 3.811 r_angle_refined_deg 2.6 r_mcangle_it 2.36 r_mcangle_other 2.36 r_angle_other_deg 2.112 r_mcbond_it 1.802 r_mcbond_other 1.801 r_chiral_restr 0.17 r_bond_refined_d 0.029 r_gen_planes_refined 0.014 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 6940 Nucleic Acid Atoms Solvent Atoms 869 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement DENZO data collection SCALEPACK data scaling MOLREP phasing PDB_EXTRACT data extraction Coot model building HKL-2000 data reduction