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Structure of the Reconstructed Ancestor of Phenolic Acid Decarboxylase AncPAD55
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ALB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 289 Protein in 10 mM MES, 150 mM NaCl, pH 6 INDEX Screen
add1: Prot 9 mg/ml
add2: Prot 6,57 mg/ml
add3: Prot 4,5 mg/ml
all drops 1 microliter
drop1: 0.5 add1 + 0.5 screen
Chrystal: INDEX Screen Condition 5
0.1 M HEPES pH 7.5 & 2.0 Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.66 53.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.999 α = 90 b = 105.274 β = 109.77 c = 81.317 γ = 90
Symmetry Space Group P 1 21 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 Bruker PHOTON III 2021-11-02 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 1.6 37.89 98.3 0.157 0.176 0.078 0.993 9.4 9.7 119233
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 1.6 1.63 1.037 1.221 0.628 0.592 5.3
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.6 37.888 119148 5970 98.588 0.232 0.2299 0.2422 0.2724 0.2807 11.102
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] -1.645 1.519 -2 2.029
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.525 r_dihedral_angle_4_deg 20.447 r_rigid_bond_restr 16.522 r_dihedral_angle_3_deg 12.201 r_dihedral_angle_1_deg 7.615 r_lrange_it 4.259 r_lrange_other 3.549 r_scangle_it 3.06 r_scangle_other 2.967 r_scbond_it 2.619
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.525 r_dihedral_angle_4_deg 20.447 r_rigid_bond_restr 16.522 r_dihedral_angle_3_deg 12.201 r_dihedral_angle_1_deg 7.615 r_lrange_it 4.259 r_lrange_other 3.549 r_scangle_it 3.06 r_scangle_other 2.967 r_scbond_it 2.619 r_scbond_other 2.569 r_mcangle_it 2.31 r_mcangle_other 2.31 r_angle_refined_deg 2.138 r_mcbond_it 1.923 r_mcbond_other 1.923 r_angle_other_deg 1.586 r_nbd_refined 0.238 r_symmetry_nbd_other 0.199 r_xyhbond_nbd_refined 0.19 r_nbtor_refined 0.175 r_symmetry_nbd_refined 0.165 r_nbd_other 0.161 r_symmetry_xyhbond_nbd_refined 0.156 r_chiral_restr 0.125 r_symmetry_xyhbond_nbd_other 0.109 r_ncsr_local_group_4 0.093 r_ncsr_local_group_3 0.091 r_ncsr_local_group_5 0.089 r_symmetry_nbtor_other 0.086 r_ncsr_local_group_2 0.086 r_ncsr_local_group_1 0.077 r_ncsr_local_group_6 0.071 r_bond_refined_d 0.02 r_gen_planes_refined 0.015 r_bond_other_d 0.004 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5468 Nucleic Acid Atoms Solvent Atoms 672 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement REFMAC refinement PHENIX model building AutoProcess data reduction AutoProcess data scaling PHENIX phasing