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Crystal structure of the M180A 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 3B35 PDB entry 3B35
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 2.62 53.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.189 α = 90 b = 108.189 β = 90 c = 97.206 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 1.46 30.63 57867
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 3B35 1.46 30.63 57867 2926 98.9 0.198 0.197 0.1949 0.226 0.2237 RANDOM 23.722
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 37.238 r_dihedral_angle_4_deg 16.968 r_dihedral_angle_3_deg 12.643 r_dihedral_angle_1_deg 5.793 r_scangle_it 2.66 r_scbond_it 1.739 r_angle_refined_deg 1.203 r_mcangle_it 1.17 r_mcbond_it 0.646 r_metal_ion_refined 0.386
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.238 r_dihedral_angle_4_deg 16.968 r_dihedral_angle_3_deg 12.643 r_dihedral_angle_1_deg 5.793 r_scangle_it 2.66 r_scbond_it 1.739 r_angle_refined_deg 1.203 r_mcangle_it 1.17 r_mcbond_it 0.646 r_metal_ion_refined 0.386 r_nbtor_refined 0.305 r_symmetry_vdw_refined 0.255 r_xyhbond_nbd_refined 0.252 r_nbd_refined 0.231 r_symmetry_hbond_refined 0.127 r_symmetry_metal_ion_refined 0.109 r_chiral_restr 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2208 Nucleic Acid Atoms Solvent Atoms 278 Heterogen Atoms 22
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction