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Crystal structure of the M180A 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 2.51 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.485 α = 90 b = 109.485 β = 90 c = 91.022 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 1.18 17.21 102599 102599
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 (All) 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 1.18 17.21 102599 5139 97.76 0.168 0.168 0.166 0.1653 0.196 0.1957 RANDOM 15.454
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] -0.03 -0.01 -0.03 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.633 r_dihedral_angle_4_deg 18.838 r_dihedral_angle_3_deg 11.304 r_sphericity_free 7.965 r_dihedral_angle_1_deg 5.95 r_sphericity_bonded 5.446 r_scangle_it 4.433 r_scbond_it 3.228 r_mcangle_it 2.528 r_mcbond_it 1.776
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.633 r_dihedral_angle_4_deg 18.838 r_dihedral_angle_3_deg 11.304 r_sphericity_free 7.965 r_dihedral_angle_1_deg 5.95 r_sphericity_bonded 5.446 r_scangle_it 4.433 r_scbond_it 3.228 r_mcangle_it 2.528 r_mcbond_it 1.776 r_rigid_bond_restr 1.715 r_angle_refined_deg 1.618 r_symmetry_hbond_refined 0.436 r_nbtor_refined 0.313 r_symmetry_vdw_refined 0.311 r_nbd_refined 0.235 r_metal_ion_refined 0.177 r_xyhbond_nbd_refined 0.175 r_symmetry_metal_ion_refined 0.17 r_chiral_restr 0.102 r_bond_refined_d 0.015 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2355 Nucleic Acid Atoms Solvent Atoms 299 Heterogen Atoms 25
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction