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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 4ALB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 289 Protein in 10mM MES, 150mM NaCl, pH6
INDEX Screen
add1: Prot 9 mg/ml
add2: Prot 6,75 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 2.65 53.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.737 α = 90 b = 104.847 β = 109.865 c = 81.495 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 DECTRIS EIGER X 4M 2021-11-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.967700 ESRF MASSIF-3
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 43.27 96.6 0.059 0.081 0.055 0.992 10.6 3.5 116814
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 1.62 0.347 0.466 0.309 0.856 3.5
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 4ALB 1.6 43.27 116559 5831 97.145 0.19 0.188 0.1878 0.2354 0.2347 17.626
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] 0.265 0.57 -0.629 -0.038
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.423 r_dihedral_angle_3_deg 12.564 r_dihedral_angle_2_deg 9.626 r_dihedral_angle_1_deg 7.448 r_rigid_bond_restr 5.886 r_lrange_it 3.856 r_lrange_other 3.417 r_scangle_it 2.715 r_scangle_other 2.704 r_mcangle_other 2.205
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.423 r_dihedral_angle_3_deg 12.564 r_dihedral_angle_2_deg 9.626 r_dihedral_angle_1_deg 7.448 r_rigid_bond_restr 5.886 r_lrange_it 3.856 r_lrange_other 3.417 r_scangle_it 2.715 r_scangle_other 2.704 r_mcangle_other 2.205 r_mcangle_it 2.204 r_scbond_it 2.154 r_scbond_other 2.149 r_angle_refined_deg 1.798 r_mcbond_it 1.788 r_mcbond_other 1.785 r_angle_other_deg 0.652 r_nbd_refined 0.207 r_symmetry_nbd_other 0.204 r_nbd_other 0.191 r_symmetry_xyhbond_nbd_refined 0.187 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.175 r_symmetry_nbd_refined 0.14 r_chiral_restr 0.106 r_symmetry_nbtor_other 0.087 r_ncsr_local_group_3 0.077 r_ncsr_local_group_2 0.076 r_ncsr_local_group_4 0.074 r_ncsr_local_group_5 0.072 r_ncsr_local_group_6 0.071 r_ncsr_local_group_1 0.066 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5452 Nucleic Acid Atoms Solvent Atoms 730 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement REFMAC refinement PHENIX model building AutoProcess data reduction AutoProcess data scaling PHENIX phasing