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Structural and Functional Relationship of Catechol-2,3-dioxygenase from Geobacillus mahadii Geo-05
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 277.15 0.1M PCTP pH 9, 25% w/v PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.04 39.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.507 α = 90 b = 68.372 β = 90 c = 142.946 γ = 90
Symmetry Space Group I 2 2 2
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 16M 2024-09-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.95374 Diamond I04
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 1.5 61.68 100 0.102 0.106 0.029 0.999 14.4 13 48633
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 1.5 1.53 100 1.191 1.239 0.339 0.788 2.4 13.2
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 1.5 61.68 46220 2410 99.99 0.1657 0.16402 0.1654 0.19726 0.1994 RANDOM 19.15
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] 1.14 -1.35 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.144 r_dihedral_angle_1_deg 6.864 r_dihedral_angle_2_deg 6.491 r_long_range_B_refined 6.13 r_long_range_B_other 6.075 r_scangle_other 4.888 r_scbond_it 3.15 r_scbond_other 3.15 r_mcangle_other 2.448 r_mcangle_it 2.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.144 r_dihedral_angle_1_deg 6.864 r_dihedral_angle_2_deg 6.491 r_long_range_B_refined 6.13 r_long_range_B_other 6.075 r_scangle_other 4.888 r_scbond_it 3.15 r_scbond_other 3.15 r_mcangle_other 2.448 r_mcangle_it 2.44 r_angle_refined_deg 1.872 r_mcbond_it 1.7 r_mcbond_other 1.699 r_angle_other_deg 0.624 r_chiral_restr 0.093 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 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 2462 Nucleic Acid Atoms Solvent Atoms 249 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement Coot model building PHASER phasing