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Biochemical and structural characterization of a novel 4-hydroxyphenylacetate-3-monooxygenase 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 293 0.8M Sodium formate, 0.1M Sodium cacodylate, 25% w/v PEG200 MME
Crystal Properties Matthews coefficient Solvent content 2.04 42.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.571 α = 90 b = 108.202 β = 99.46 c = 99.055 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 X 16M 2024-08-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.953738 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 2.4 108.2 100 0.188 0.203 0.078 0.992 6.9 6.7 73743
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 2.4 2.45 99.7 1.262 1.389 0.801 0.589 1.6 5.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.4 97.9 70078 3637 99.95 0.18714 0.18398 0.24989 0.2439 RANDOM 37.125
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] 1.55 0.11 -1.03 -0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.986 r_dihedral_angle_2_deg 12.165 r_dihedral_angle_1_deg 6.907 r_long_range_B_refined 4.543 r_long_range_B_other 4.543 r_scangle_other 3.612 r_mcangle_it 2.528 r_mcangle_other 2.528 r_scbond_it 2.268 r_scbond_other 2.268
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.986 r_dihedral_angle_2_deg 12.165 r_dihedral_angle_1_deg 6.907 r_long_range_B_refined 4.543 r_long_range_B_other 4.543 r_scangle_other 3.612 r_mcangle_it 2.528 r_mcangle_other 2.528 r_scbond_it 2.268 r_scbond_other 2.268 r_angle_refined_deg 1.704 r_mcbond_it 1.655 r_mcbond_other 1.655 r_angle_other_deg 0.587 r_chiral_restr 0.08 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_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 15417 Nucleic Acid Atoms Solvent Atoms 121 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement Aimless data scaling DIALS data reduction PHASER phasing