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Ancestral L-tryptophan synthase beta-subunit 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 296 20% w/v PEG 3350, 200mM ammonium formate
Crystal Properties Matthews coefficient Solvent content 2.13 42.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.529 α = 90 b = 91.661 β = 105.27 c = 105.181 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 PILATUS3 6M 2022-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.7 47.21 99.3 1 23.8 13.4 160314
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.79 0.816
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 (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 1.7 47.21 152410 7877 99.13 0.19216 0.19046 0.199 0.225 0.2324 RANDOM 25.036
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.144 r_dihedral_angle_2_deg 8.584 r_dihedral_angle_1_deg 7.008 r_long_range_B_refined 5.574 r_long_range_B_other 5.561 r_scangle_other 4.633 r_scbond_it 3.084 r_scbond_other 3.084 r_mcangle_it 2.99 r_mcangle_other 2.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.144 r_dihedral_angle_2_deg 8.584 r_dihedral_angle_1_deg 7.008 r_long_range_B_refined 5.574 r_long_range_B_other 5.561 r_scangle_other 4.633 r_scbond_it 3.084 r_scbond_other 3.084 r_mcangle_it 2.99 r_mcangle_other 2.99 r_mcbond_it 2.21 r_mcbond_other 2.209 r_angle_refined_deg 1.76 r_angle_other_deg 0.621 r_chiral_restr 0.091 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 12099 Nucleic Acid Atoms Solvent Atoms 498 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling MOLREP phasing