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Aromatic aminotransferase AroH (Aro8) form Aspergillus fumigatus in complex with PLP (internal aldimine)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JE5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 294 Optimization of hit G4 of the Molecular Dimension Morpheus screen :
0.1M (Sodium formate; Ammonium
acetate; Sodium citrate tribasic
dihydrate; Potassium sodium tartrate
tetrahydrate; Sodium oxamate); 50mM Imidazole; 50mMES
monohydrate (acid);
13.7% v/v MPD; 13.7% PEG
1000; 13.7% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.28 46.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.209 α = 84.77 b = 75.26 β = 87.51 c = 121.631 γ = 65.37
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 DECTRIS PILATUS 6M 2019-05-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.0 ELETTRA 11.2C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.4 47.2 97.2 0.109 0.127 0.065 0.992 6.3 3.8 78375
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.45 97.5 0.781 0.904 0.451 0.597 4
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 4JE5 2.4 47.2 74503 3871 97.22 0.248 0.2455 0.2459 0.2935 0.2903 RANDOM 52.302
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] 4.56 0.48 0.03 -0.82 -0.16 -2.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.805 r_dihedral_angle_3_deg 18.589 r_dihedral_angle_4_deg 17.234 r_dihedral_angle_1_deg 5.333 r_angle_other_deg 2.436 r_angle_refined_deg 1.224 r_chiral_restr 0.059 r_bond_other_d 0.036 r_bond_refined_d 0.004 r_gen_planes_other 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.805 r_dihedral_angle_3_deg 18.589 r_dihedral_angle_4_deg 17.234 r_dihedral_angle_1_deg 5.333 r_angle_other_deg 2.436 r_angle_refined_deg 1.224 r_chiral_restr 0.059 r_bond_other_d 0.036 r_bond_refined_d 0.004 r_gen_planes_other 0.004 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14565 Nucleic Acid Atoms Solvent Atoms 166 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing PDB_EXTRACT data extraction