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crystal structure of the L136 aminotransferase from acanthamoeba polyphaga mimivirus in complex with the TDP-viosamine external aldimine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7MFP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 protein incubated with 1 mM PLP and 5 MM TDP-viosamine
18-22% PEG-3350, 2% MPD, 100 mM MES
Crystal Properties Matthews coefficient Solvent content 2.25 45.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.21 α = 90 b = 108.515 β = 90 c = 146.058 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 2019-10-22 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 1.95 50 99.8 0.09 16.2 10.7 105900
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 1.95 2.05 99.7 0.411 3.5 5.1
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 7mfp 1.95 29.052 105900 5323 99.829 0.176 0.1733 0.1814 0.2222 0.2269 14.791
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] -0.008 -0.001 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.333 r_dihedral_angle_4_deg 19.747 r_dihedral_angle_3_deg 14.594 r_dihedral_angle_1_deg 7.009 r_lrange_it 4.33 r_lrange_other 4.33 r_scangle_it 2.588 r_scangle_other 2.588 r_mcangle_it 1.82 r_mcangle_other 1.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.333 r_dihedral_angle_4_deg 19.747 r_dihedral_angle_3_deg 14.594 r_dihedral_angle_1_deg 7.009 r_lrange_it 4.33 r_lrange_other 4.33 r_scangle_it 2.588 r_scangle_other 2.588 r_mcangle_it 1.82 r_mcangle_other 1.82 r_scbond_it 1.586 r_scbond_other 1.586 r_angle_refined_deg 1.496 r_angle_other_deg 1.328 r_mcbond_it 1.121 r_mcbond_other 1.121 r_nbd_refined 0.209 r_nbd_other 0.191 r_xyhbond_nbd_refined 0.19 r_symmetry_nbd_other 0.182 r_symmetry_xyhbond_nbd_refined 0.179 r_nbtor_refined 0.171 r_symmetry_nbd_refined 0.134 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.072 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_symmetry_xyhbond_nbd_other 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11178 Nucleic Acid Atoms Solvent Atoms 1236 Heterogen Atoms 226
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling PHASER phasing