☰ Navigation Tabs
Crystal structure of ancestral L-galactono-1,4-lactone dehydrogenase: A113G variant
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% PEG 3350, 0.2 M Lithium Nitrate
Crystal Properties Matthews coefficient Solvent content 2.17 43.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.387 α = 90 b = 69.657 β = 98.29 c = 67.608 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 2023-03-31 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 1.7 66.9 98.9 0.092 0.102 0.043 0.998 10.7 5.5 53389
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 1.7 1.73 99.4 1.336 1.477 0.618 0.593 5.5
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 66.9 50741 2623 98.84 0.18036 0.17874 0.191 0.21192 0.2223 RANDOM 25.772
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] -0.12 -1.31 0.24 0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.748 r_dihedral_angle_4_deg 16.474 r_dihedral_angle_3_deg 13.819 r_long_range_B_refined 6.961 r_long_range_B_other 6.941 r_dihedral_angle_1_deg 6.922 r_scangle_other 5.447 r_mcangle_it 3.689 r_mcangle_other 3.688 r_scbond_it 3.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.748 r_dihedral_angle_4_deg 16.474 r_dihedral_angle_3_deg 13.819 r_long_range_B_refined 6.961 r_long_range_B_other 6.941 r_dihedral_angle_1_deg 6.922 r_scangle_other 5.447 r_mcangle_it 3.689 r_mcangle_other 3.688 r_scbond_it 3.56 r_scbond_other 3.56 r_mcbond_other 2.499 r_mcbond_it 2.498 r_angle_refined_deg 1.678 r_angle_other_deg 1.401 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 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 3823 Nucleic Acid Atoms Solvent Atoms 295 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement Aimless data scaling