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Crystal structure of the S228A mutant of the aminopeptidase from Vibrio proteolyticus in complex with leucine phosphonic acid
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, NaCl, KSCN, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.53 51.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.907 α = 90 b = 109.907 β = 90 c = 91.095 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 1.75 20.37 32789 32789
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 1.75 20.37 32789 1655 98.74 0.178 0.177 0.1773 0.209 0.2101 RANDOM 14.089
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.933 r_dihedral_angle_4_deg 20.195 r_dihedral_angle_3_deg 12.138 r_dihedral_angle_1_deg 5.856 r_scangle_it 3.23 r_scbond_it 2.071 r_angle_refined_deg 1.283 r_mcangle_it 1.185 r_mcbond_it 0.675 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.933 r_dihedral_angle_4_deg 20.195 r_dihedral_angle_3_deg 12.138 r_dihedral_angle_1_deg 5.856 r_scangle_it 3.23 r_scbond_it 2.071 r_angle_refined_deg 1.283 r_mcangle_it 1.185 r_mcbond_it 0.675 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.224 r_nbd_refined 0.216 r_metal_ion_refined 0.216 r_symmetry_hbond_refined 0.143 r_xyhbond_nbd_refined 0.136 r_symmetry_metal_ion_refined 0.127 r_chiral_restr 0.088 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2263 Nucleic Acid Atoms Solvent Atoms 250 Heterogen Atoms 8
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction MOLREP phasing