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X-ray structure of the L136 Aminotransferase from Acanthamoeba polyphaga mimivirus in the presence of TDP and PMP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 7.5 293 protein incubated with 1 mM PLP and 5 mM TDP-4-aminoquinovose.
11-14% PEG-8000, 200 mM KCl, 100 mM HEPES
Crystal Properties Matthews coefficient Solvent content 2.43 49.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.885 α = 90 b = 126.875 β = 90.89 c = 206.365 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 210r 2018-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.9790 APS 19-BM
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 1.7 50 94.3 0.055 36.2 4.1 397722
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 1.7 1.73 87.4 0.194 5 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.7 33.78 377894 19828 94.23 0.1839 0.1819 0.1923 0.2215 0.2296 RANDOM 24.036
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] 2.12 -0.32 -0.64 -1.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.642 r_dihedral_angle_4_deg 18.411 r_dihedral_angle_3_deg 14.912 r_dihedral_angle_1_deg 6.817 r_angle_refined_deg 1.619 r_angle_other_deg 1.411 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.642 r_dihedral_angle_4_deg 18.411 r_dihedral_angle_3_deg 14.912 r_dihedral_angle_1_deg 6.817 r_angle_refined_deg 1.619 r_angle_other_deg 1.411 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 28003 Nucleic Acid Atoms Solvent Atoms 2914 Heterogen Atoms 448
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling PHASER phasing