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A novel aminotransferase from Streptomyces sp.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6GWI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 6.5 292.15 0.2 M Potassium thiocyanate
0.1 M Bis-Tris propane 6.5
20 % w/v PEG 3350
1 mM PLP
Crystal Properties Matthews coefficient Solvent content 2.04 39.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.32 α = 90 b = 176.1 β = 90 c = 60.85 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 113.15 PIXEL DECTRIS EIGER2 XE 16M 2022-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
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 1.49 60.85 81.38 0.041 0.043 0.012 1 31.8 10.33 112260 11.89
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 1.49 1.52 10.66 0.192 0.269 0.188 0.9 2.3
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.49 60.85 112259 5565 81.383 0.13 0.1285 0.1287 0.1585 0.1592 16.655
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] 0.091 -0.904 0.813
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.838 r_dihedral_angle_3_deg 11.563 r_dihedral_angle_2_deg 7.92 r_dihedral_angle_1_deg 6.108 r_lrange_it 5.751 r_lrange_other 5.751 r_scangle_it 3.644 r_scangle_other 3.611 r_scbond_it 2.451 r_scbond_other 2.423
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.838 r_dihedral_angle_3_deg 11.563 r_dihedral_angle_2_deg 7.92 r_dihedral_angle_1_deg 6.108 r_lrange_it 5.751 r_lrange_other 5.751 r_scangle_it 3.644 r_scangle_other 3.611 r_scbond_it 2.451 r_scbond_other 2.423 r_mcangle_it 2.157 r_mcangle_other 2.157 r_angle_refined_deg 1.842 r_mcbond_it 1.457 r_mcbond_other 1.457 r_angle_other_deg 0.655 r_symmetry_nbd_refined 0.297 r_nbd_other 0.265 r_nbd_refined 0.227 r_symmetry_xyhbond_nbd_refined 0.198 r_symmetry_nbd_other 0.189 r_nbtor_refined 0.187 r_xyhbond_nbd_refined 0.162 r_xyhbond_nbd_other 0.126 r_symmetry_xyhbond_nbd_other 0.101 r_chiral_restr 0.1 r_symmetry_nbtor_other 0.079 r_ncsr_local_group_1 0.076 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7094 Nucleic Acid Atoms Solvent Atoms 1169 Heterogen Atoms 95
Software Software Software Name Purpose REFMAC refinement xia2 data reduction XSCALE data scaling MoRDa phasing