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Crystal structure of monomeric PLP-dependent transaminase from Desulfobacula toluolica in P 21 21 21 space group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 288 0.1M Ammonium acetate, 0.1M Bis-tris pH 5.5, 17% PEG 10000
Crystal Properties Matthews coefficient Solvent content 1.97 37.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.847 α = 90 b = 56.226 β = 90 c = 118.625 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 DECTRIS EIGER X 16M 2021-11-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.88560 ESRF ID23-1
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 1.79 40.81 98.8 0.047 0.056 0.028 0.998 13.4 3.6 24352
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 1.79 1.83 96.2 0.67 0.787 0.405 0.686 3.4
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 MOLECULAR REPLACEMENT THROUGHOUT 1.79 40.81 23150 1146 98.51 0.19522 0.19325 0.2005 0.23575 0.239 RANDOM 38.029
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] -0.15 -0.8 0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.653 r_dihedral_angle_4_deg 18.155 r_dihedral_angle_3_deg 15.413 r_long_range_B_other 9.677 r_long_range_B_refined 9.664 r_scangle_other 7.953 r_dihedral_angle_1_deg 7.366 r_mcangle_it 6.148 r_mcangle_other 6.146 r_scbond_it 5.892
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.653 r_dihedral_angle_4_deg 18.155 r_dihedral_angle_3_deg 15.413 r_long_range_B_other 9.677 r_long_range_B_refined 9.664 r_scangle_other 7.953 r_dihedral_angle_1_deg 7.366 r_mcangle_it 6.148 r_mcangle_other 6.146 r_scbond_it 5.892 r_scbond_other 5.889 r_mcbond_other 4.779 r_mcbond_it 4.776 r_angle_refined_deg 2.1 r_angle_other_deg 1.501 r_chiral_restr 0.105 r_bond_refined_d 0.016 r_gen_planes_refined 0.013 r_gen_planes_other 0.004 r_bond_other_d 0.003 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1872 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement Aimless data scaling DIALS data reduction MOLREP phasing PDB_EXTRACT data extraction