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Crystal structure of ancestral L-galactono-1,4-lactone dehydrogenase: in complex with L-galactono-1,4-lactone
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 293.15 20% PEG3350, 0.2 M Lithium Nitrate
Crystal Properties Matthews coefficient Solvent content 2.43 49.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.527 α = 90 b = 69.964 β = 103.72 c = 71.239 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 R 4M 2023-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.9677 ESRF ID30B
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 2.1 49.25 98.4 0.096 0.101 0.031 0.999 13.9 10.6 31671
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 2.1 2.16 99 1.891 1.992 0.62 0.787 10.1
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 2.1 49.25 30085 1570 98.3 0.20225 0.19959 0.2113 0.25433 0.2665 RANDOM 46.393
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] 3.45 -5.64 0.57 -1.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.578 r_dihedral_angle_4_deg 17.519 r_dihedral_angle_3_deg 15.271 r_long_range_B_refined 7.783 r_long_range_B_other 7.782 r_dihedral_angle_1_deg 7.134 r_scangle_other 5.911 r_mcangle_it 4.916 r_mcangle_other 4.915 r_scbond_it 3.877
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.578 r_dihedral_angle_4_deg 17.519 r_dihedral_angle_3_deg 15.271 r_long_range_B_refined 7.783 r_long_range_B_other 7.782 r_dihedral_angle_1_deg 7.134 r_scangle_other 5.911 r_mcangle_it 4.916 r_mcangle_other 4.915 r_scbond_it 3.877 r_scbond_other 3.876 r_mcbond_it 3.321 r_mcbond_other 3.321 r_angle_refined_deg 1.49 r_angle_other_deg 1.245 r_chiral_restr 0.19 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 3754 Nucleic Acid Atoms Solvent Atoms 131 Heterogen Atoms 65
Software Software Software Name Purpose REFMAC refinement Aimless data scaling