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Crystal structure of the S228A mutant of the aminopeptidase from Vibrio proteolyticus in complex with leucine
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 2.57 52.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.549 α = 90 b = 110.549 β = 90 c = 91.626 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 14.98 30654 30654
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 14.98 30654 1574 90.69 0.196 0.194 0.1945 0.234 0.2352 RANDOM 27.352
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.679 r_dihedral_angle_4_deg 23.2 r_dihedral_angle_3_deg 13.99 r_dihedral_angle_1_deg 6.27 r_scangle_it 3.492 r_scbond_it 2.269 r_angle_refined_deg 1.463 r_mcangle_it 1.445 r_mcbond_it 0.838 r_symmetry_metal_ion_refined 0.612
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.679 r_dihedral_angle_4_deg 23.2 r_dihedral_angle_3_deg 13.99 r_dihedral_angle_1_deg 6.27 r_scangle_it 3.492 r_scbond_it 2.269 r_angle_refined_deg 1.463 r_mcangle_it 1.445 r_mcbond_it 0.838 r_symmetry_metal_ion_refined 0.612 r_symmetry_hbond_refined 0.39 r_nbtor_refined 0.306 r_symmetry_vdw_refined 0.275 r_nbd_refined 0.217 r_metal_ion_refined 0.191 r_xyhbond_nbd_refined 0.154 r_chiral_restr 0.099 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2213 Nucleic Acid Atoms Solvent Atoms 261 Heterogen Atoms 16
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction MOLREP phasing