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Crystal structure of monomeric PLP-dependent transaminase from Desulfobacula toluolica in F 41 3 2 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 400mM NaNitrate, 0.1M Bis-tris propane pH 6.5, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 5.08 75.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 250.089 α = 90 b = 250.089 β = 90 c = 250.089 γ = 90
Symmetry Space Group F 41 3 2
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 2021-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.89999 SPring-8 BL41XU
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 2.58 144.39 100 0.191 0.192 0.023 0.998 17.3 66.9 21699
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 2.58 2.69 100 9.059 9.174 1.437 0.446 37.6
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 2.58 88.58 20573 1096 99.97 0.21116 0.20912 0.2091 0.25274 0.2531 RANDOM 98.156
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.086 r_dihedral_angle_4_deg 26.33 r_dihedral_angle_3_deg 23.405 r_long_range_B_refined 15.752 r_mcangle_it 11.131 r_scbond_it 10.553 r_dihedral_angle_1_deg 10.173 r_mcbond_it 8.228 r_angle_refined_deg 3.474 r_chiral_restr 0.293
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.086 r_dihedral_angle_4_deg 26.33 r_dihedral_angle_3_deg 23.405 r_long_range_B_refined 15.752 r_mcangle_it 11.131 r_scbond_it 10.553 r_dihedral_angle_1_deg 10.173 r_mcbond_it 8.228 r_angle_refined_deg 3.474 r_chiral_restr 0.293 r_bond_refined_d 0.019 r_gen_planes_refined 0.017 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2238 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement Aimless data scaling DIALS data reduction MOLREP phasing PDB_EXTRACT data extraction