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Structure of the Reconstructed Ancestor of Phenolic Acid Decarboxylase AncPAD31
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4UU3 4UU3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 289 5 mg/ml AncPAD31, Index screen 74, 0.2 M Lithium sulfate monohydrate, 0.1 M BIS-TRIS, 25% w/v Polyethylene glycol 3,350
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.069 α = 90 b = 59.971 β = 90 c = 105.1 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 Bruker PHOTON III 2021-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 LIQUID ANODE BRUKER METALJET 1.34138
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 2.7 34.98 99.9 0.135 0.157 0.078 0.995 5.6 6.7 7936
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 2.7 2.83 0.867 1.011 0.508 0.703 6.8
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4UU3 2.7 34.98 7901 384 99.899 0.214 0.2102 0.2104 0.2841 0.284 47.72
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] -0.656 1.492 -0.835
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.918 r_dihedral_angle_4_deg 27.369 r_dihedral_angle_3_deg 19.109 r_lrange_it 13.719 r_lrange_other 13.705 r_scangle_other 10.634 r_scangle_it 10.633 r_dihedral_angle_1_deg 8.922 r_mcangle_it 8.382 r_mcangle_other 8.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.918 r_dihedral_angle_4_deg 27.369 r_dihedral_angle_3_deg 19.109 r_lrange_it 13.719 r_lrange_other 13.705 r_scangle_other 10.634 r_scangle_it 10.633 r_dihedral_angle_1_deg 8.922 r_mcangle_it 8.382 r_mcangle_other 8.38 r_scbond_it 7.26 r_scbond_other 7.253 r_mcbond_it 6.018 r_mcbond_other 6.007 r_angle_other_deg 2.457 r_angle_refined_deg 2.124 r_nbd_other 0.288 r_symmetry_nbd_other 0.217 r_symmetry_xyhbond_nbd_refined 0.204 r_nbd_refined 0.197 r_nbtor_refined 0.173 r_symmetry_nbd_refined 0.161 r_ncsr_local_group_1 0.157 r_xyhbond_nbd_refined 0.143 r_chiral_restr 0.103 r_symmetry_nbtor_other 0.083 r_symmetry_xyhbond_nbd_other 0.062 r_bond_other_d 0.035 r_gen_planes_other 0.017 r_bond_refined_d 0.014 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2603 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement REFMAC refinement PROTEUM data reduction PROTEUM data scaling PHASER phasing