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Structure of the Reconstructed Ancestor of Phenolic Acid Decarboxylase AncPAD134
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4UU3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 5 mg/ml AncPAD134, Index screen, condition 76 (0.2 Lithium sulfate, 0.1 M HEPES pH 7.5, 25 % w/v PEG 3,350)
Crystal Properties Matthews coefficient Solvent content 2.31 46.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.321 α = 90 b = 106.679 β = 90 c = 114.752 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 2021-11-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 LIQUID ANODE Excillum MetalJet D2+ 70 kV 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 2.67 35.95 99.9 0.162 0.174 0.063 0.997 12.9 14.1 34625
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 2.67 2.8 0.919 0.999 0.388 0.876 12.3
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 2.67 35.949 34565 1774 99.89 0.193 0.1906 0.1906 0.229 0.2291 37.275
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] -0.072 -0.175 0.247
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.042 r_dihedral_angle_4_deg 14.655 r_dihedral_angle_3_deg 13.418 r_dihedral_angle_1_deg 7.538 r_lrange_it 7.534 r_scangle_it 5.346 r_mcangle_it 4.956 r_scbond_it 3.476 r_mcbond_it 3.251 r_angle_refined_deg 1.549
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.042 r_dihedral_angle_4_deg 14.655 r_dihedral_angle_3_deg 13.418 r_dihedral_angle_1_deg 7.538 r_lrange_it 7.534 r_scangle_it 5.346 r_mcangle_it 4.956 r_scbond_it 3.476 r_mcbond_it 3.251 r_angle_refined_deg 1.549 r_nbtor_refined 0.294 r_symmetry_nbd_refined 0.223 r_nbd_refined 0.207 r_symmetry_xyhbond_nbd_refined 0.194 r_xyhbond_nbd_refined 0.132 r_chiral_restr 0.075 r_bond_refined_d 0.014 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8002 Nucleic Acid Atoms Solvent Atoms 273 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PROTEUM data reduction PROTEUM data scaling MOLREP phasing