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Crystal structure of the M180A 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 2.49 50.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.148 α = 90 b = 109.148 β = 90 c = 90.99 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) R Merge I (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 1.1 41 0.059 122065 14.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.1 2
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 1.1 41 122065 6145 95.04 0.15 0.149 0.1494 0.166 0.1653 RANDOM 14.646
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 37.163 r_dihedral_angle_4_deg 18.861 r_dihedral_angle_3_deg 11.358 r_sphericity_free 8.116 r_dihedral_angle_1_deg 6.317 r_sphericity_bonded 4.131 r_scangle_it 3.425 r_scbond_it 2.516 r_mcangle_it 1.892 r_angle_refined_deg 1.533
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.163 r_dihedral_angle_4_deg 18.861 r_dihedral_angle_3_deg 11.358 r_sphericity_free 8.116 r_dihedral_angle_1_deg 6.317 r_sphericity_bonded 4.131 r_scangle_it 3.425 r_scbond_it 2.516 r_mcangle_it 1.892 r_angle_refined_deg 1.533 r_rigid_bond_restr 1.44 r_mcbond_it 1.313 r_symmetry_vdw_refined 0.31 r_nbtor_refined 0.306 r_nbd_refined 0.285 r_symmetry_hbond_refined 0.256 r_xyhbond_nbd_refined 0.227 r_chiral_restr 0.101 r_metal_ion_refined 0.077 r_bond_refined_d 0.012 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2522 Nucleic Acid Atoms Solvent Atoms 360 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction SCALEPACK data scaling MOLREP phasing