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Crystal structure of E. coli Aminopeptidase N in complex with Phenylalanine
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 7 298 2M Sodium Malonate, pH=7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.53 65.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.582 α = 90 b = 120.582 β = 90 c = 170.761 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 KOHZU: Double Crystal Si(111) 2007-01-25 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1.0 ALS 8.2.2
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 1.3 50 99.2 0.123 8.2 8.9 346171 2 2 14.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.32 89.9 0.49 0.49 1.18 1.9 15484
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT 2HPO 1.3 50 487111 339183 10333 97.16 0.177 0.177 0.1767 0.19416 Random 18.757
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] 0.05 0.03 0.05 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.853 r_dihedral_angle_4_deg 17.004 r_dihedral_angle_3_deg 12.202 r_dihedral_angle_1_deg 5.557 r_sphericity_bonded 4.396 r_sphericity_free 3.732 r_scangle_it 3.342 r_scbond_it 3.078 r_rigid_bond_restr 3.061 r_mcangle_it 1.356
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.853 r_dihedral_angle_4_deg 17.004 r_dihedral_angle_3_deg 12.202 r_dihedral_angle_1_deg 5.557 r_sphericity_bonded 4.396 r_sphericity_free 3.732 r_scangle_it 3.342 r_scbond_it 3.078 r_rigid_bond_restr 3.061 r_mcangle_it 1.356 r_angle_refined_deg 1.15 r_mcbond_it 0.804 r_nbtor_refined 0.296 r_nbd_refined 0.197 r_symmetry_vdw_refined 0.164 r_symmetry_hbond_refined 0.149 r_metal_ion_refined 0.14 r_xyhbond_nbd_refined 0.131 r_chiral_restr 0.081 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6940 Nucleic Acid Atoms Solvent Atoms 1113 Heterogen Atoms 77
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction BOS data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing