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Crystal structure of the S228A 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 50.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.317 α = 90 b = 109.317 β = 90 c = 91.003 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 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 1.22 21.72 92234 92234
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 1.22 21.72 92234 4637 97.3 0.15 0.149 0.1583 0.171 0.1783 RANDOM 15.041
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] -0.1 -0.05 -0.1 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.866 r_dihedral_angle_4_deg 19.001 r_sphericity_free 13.922 r_dihedral_angle_3_deg 11.825 r_sphericity_bonded 7.834 r_dihedral_angle_1_deg 6.371 r_scangle_it 4.996 r_scbond_it 3.599 r_mcangle_it 2.58 r_mcbond_it 1.819
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.866 r_dihedral_angle_4_deg 19.001 r_sphericity_free 13.922 r_dihedral_angle_3_deg 11.825 r_sphericity_bonded 7.834 r_dihedral_angle_1_deg 6.371 r_scangle_it 4.996 r_scbond_it 3.599 r_mcangle_it 2.58 r_mcbond_it 1.819 r_rigid_bond_restr 1.746 r_angle_refined_deg 1.67 r_mcbond_other 1.24 r_angle_other_deg 1.019 r_symmetry_vdw_other 0.324 r_symmetry_vdw_refined 0.297 r_nbd_refined 0.259 r_xyhbond_nbd_refined 0.228 r_symmetry_hbond_refined 0.227 r_nbd_other 0.209 r_nbtor_refined 0.181 r_chiral_restr 0.105 r_nbtor_other 0.089 r_metal_ion_refined 0.034 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2382 Nucleic Acid Atoms Solvent Atoms 218 Heterogen Atoms 19
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction MOLREP phasing