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Crystal structure of the D118N mutant of the aminopeptidase from Vibrio proteolyticus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AMP PDB entry 1AMP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 HEPES, KSCN, NaCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.5 50.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.294 α = 90 b = 109.294 β = 90 c = 91.009 γ = 120
Symmetry Space Group P 61 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.90010 APS 14-BM-C
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 1.17 42 102258 102258
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 PDB entry 1AMP 1.17 42 102258 5101 95.35 0.143 0.142 0.1516 0.161 0.1694 RANDOM 11.391
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] 0.01 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.091 r_dihedral_angle_4_deg 22.371 r_dihedral_angle_3_deg 11.263 r_sphericity_free 9.694 r_dihedral_angle_1_deg 6.114 r_sphericity_bonded 5.079 r_scangle_it 4.328 r_scbond_it 3.047 r_mcangle_it 2.209 r_symmetry_metal_ion_refined 1.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.091 r_dihedral_angle_4_deg 22.371 r_dihedral_angle_3_deg 11.263 r_sphericity_free 9.694 r_dihedral_angle_1_deg 6.114 r_sphericity_bonded 5.079 r_scangle_it 4.328 r_scbond_it 3.047 r_mcangle_it 2.209 r_symmetry_metal_ion_refined 1.62 r_angle_refined_deg 1.617 r_mcbond_it 1.532 r_rigid_bond_restr 1.525 r_angle_other_deg 0.968 r_mcbond_other 0.851 r_symmetry_vdw_refined 0.423 r_symmetry_vdw_other 0.371 r_nbd_refined 0.242 r_nbd_other 0.201 r_xyhbond_nbd_refined 0.191 r_nbtor_refined 0.181 r_symmetry_hbond_refined 0.179 r_chiral_restr 0.097 r_nbtor_other 0.09 r_metal_ion_refined 0.05 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2321 Nucleic Acid Atoms Solvent Atoms 292 Heterogen Atoms 20
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction