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Crystal structure of ancestral L-galactono-1,4-lactone dehydrogenase: G413N variant in complex with L-gulono-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 49.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.28 α = 90 b = 70.026 β = 102.16 c = 69.631 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 PILATUS 6M 2023-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.9655 ESRF ID23-1
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 2.3 70.03 92.4 0.035 0.043 0.024 0.999 8.9 2.9 22213
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 2.3 2.38 98 0.684 0.833 0.469 0.739 2.9
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 2.3 48.86 21138 1053 92.17 0.20731 0.20348 0.2157 0.28311 0.2919 RANDOM 63.461
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] 1.32 -6.43 -0.27 1.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.292 r_dihedral_angle_4_deg 17.758 r_dihedral_angle_3_deg 17.5 r_long_range_B_other 10.655 r_long_range_B_refined 10.634 r_scangle_other 7.655 r_dihedral_angle_1_deg 7.649 r_mcangle_it 7.284 r_mcangle_other 7.282 r_scbond_it 5.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.292 r_dihedral_angle_4_deg 17.758 r_dihedral_angle_3_deg 17.5 r_long_range_B_other 10.655 r_long_range_B_refined 10.634 r_scangle_other 7.655 r_dihedral_angle_1_deg 7.649 r_mcangle_it 7.284 r_mcangle_other 7.282 r_scbond_it 5.06 r_scbond_other 5.059 r_mcbond_it 4.997 r_mcbond_other 4.994 r_angle_refined_deg 1.494 r_angle_other_deg 1.19 r_chiral_restr 0.062 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 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 3764 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms 65
Software Software Software Name Purpose REFMAC refinement Aimless data scaling