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crystal structure of the L136 aminotransferase K185A from acanthamoeba polyphaga mimivirus in the presence of the UDP-viosamine external aldimine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7MFO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 protein incubated with 1 mM PLP and 5 mM UDP-viosamine
18-22% PEG-3350, 2% MPD, 100 mM MES
Crystal Properties Matthews coefficient Solvent content 2.23 44.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.033 α = 90 b = 108.548 β = 90 c = 145.514 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL Bruker PHOTON II 2019-09-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER D8 QUEST 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.85 50 99.8 0.084 15.4 8 123055
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.9 99.3 0.443 4 3
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7mfo 1.85 29.723 123059 6181 99.751 0.174 0.1718 0.1796 0.2187 0.2235 12.803
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] -0.015 -0.003 0.017
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.434 r_dihedral_angle_4_deg 15.462 r_dihedral_angle_3_deg 14.713 r_dihedral_angle_1_deg 6.955 r_lrange_it 4.188 r_lrange_other 4.188 r_scangle_it 2.499 r_scangle_other 2.499 r_mcangle_it 1.684 r_mcangle_other 1.684
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.434 r_dihedral_angle_4_deg 15.462 r_dihedral_angle_3_deg 14.713 r_dihedral_angle_1_deg 6.955 r_lrange_it 4.188 r_lrange_other 4.188 r_scangle_it 2.499 r_scangle_other 2.499 r_mcangle_it 1.684 r_mcangle_other 1.684 r_angle_refined_deg 1.613 r_scbond_it 1.547 r_scbond_other 1.547 r_angle_other_deg 1.366 r_mcbond_it 1.049 r_mcbond_other 1.048 r_metal_ion_refined 0.258 r_symmetry_nbd_refined 0.222 r_symmetry_xyhbond_nbd_refined 0.214 r_nbd_refined 0.212 r_xyhbond_nbd_refined 0.193 r_nbd_other 0.188 r_symmetry_nbd_other 0.177 r_nbtor_refined 0.172 r_symmetry_xyhbond_nbd_other 0.166 r_chiral_restr 0.079 r_symmetry_nbtor_other 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11213 Nucleic Acid Atoms Solvent Atoms 1354 Heterogen Atoms 234
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling PHASER phasing