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An unexpected vestigial protein complex reveals the evolutionary origins of an s-triazine catabolic enzyme.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IP4 3ip4 and 3dha experimental model PDB 3DHA 3ip4 and 3dha
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 281 100mM bis-tris at pH 6.0, 276 mM MgCl2, 17.6 (w/v) PEG 8000 in the reservoir with protein at 1.1 mg/mL with 0.05% agarose gel in 250 plus 250 nL drops at 8 C.
Crystal Properties Matthews coefficient Solvent content 2.21 44.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.489 α = 90 b = 89.04 β = 101.89 c = 141.672 γ = 90
Symmetry Space Group I 1 2 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 PIXEL DECTRIS EIGER X 16M 2017-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.99989 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.95 69.3 100 0.233 0.095 0.991 6.9 6.9 70426
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 1.99 100 1.545 0.622 0.804 7.1
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 3ip4 and 3dha 1.95 69.3 66810 3434 99.74 0.15478 0.15294 0.1675 0.19066 0.2013 RANDOM 17.54
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] 2.46 -1.11 -0.62 -1.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.046 r_dihedral_angle_4_deg 16.305 r_dihedral_angle_3_deg 12.496 r_dihedral_angle_1_deg 5.956 r_long_range_B_refined 5.223 r_long_range_B_other 5.144 r_scangle_other 3.893 r_scbond_it 2.541 r_scbond_other 2.54 r_mcangle_it 2.237
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.046 r_dihedral_angle_4_deg 16.305 r_dihedral_angle_3_deg 12.496 r_dihedral_angle_1_deg 5.956 r_long_range_B_refined 5.223 r_long_range_B_other 5.144 r_scangle_other 3.893 r_scbond_it 2.541 r_scbond_other 2.54 r_mcangle_it 2.237 r_mcangle_other 2.237 r_angle_refined_deg 1.726 r_mcbond_it 1.494 r_mcbond_other 1.493 r_angle_other_deg 1.031 r_chiral_restr 0.109 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 7780 Nucleic Acid Atoms Solvent Atoms 726 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MoRDa phasing