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Crystal Structure of Decarboxylative Vanillate 1-Hydroxylase from Phanerochaete chrysosporium
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 6.5 277.15 0.2M Calcium acetate hydrate, 0.1 M Sodium cacodylate trihydrate, 18% (w/v) Polyethylene glycol 8,000
Crystal Properties Matthews coefficient Solvent content 2.21 44.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.632 α = 90 b = 97.13 β = 90 c = 106.596 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS3 S 6M 2021-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
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 48.56 100 0.054 0.056 0.015 1 30.3 13.1 53038
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 1.73 100 0.872 0.906 0.244 0.905 13.6
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 46.77 31127 1697 99.99 0.18174 0.17991 0.191 0.21475 0.2214 RANDOM 27.898
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] 0.03 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.129 r_dihedral_angle_4_deg 18.016 r_dihedral_angle_3_deg 15.899 r_dihedral_angle_1_deg 6.537 r_long_range_B_other 5.875 r_long_range_B_refined 5.874 r_scangle_other 4.791 r_scbond_it 3.214 r_scbond_other 3.213 r_mcangle_it 2.805
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.129 r_dihedral_angle_4_deg 18.016 r_dihedral_angle_3_deg 15.899 r_dihedral_angle_1_deg 6.537 r_long_range_B_other 5.875 r_long_range_B_refined 5.874 r_scangle_other 4.791 r_scbond_it 3.214 r_scbond_other 3.213 r_mcangle_it 2.805 r_mcangle_other 2.804 r_mcbond_it 2.155 r_mcbond_other 2.147 r_angle_refined_deg 1.641 r_angle_other_deg 1.436 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 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 3348 Nucleic Acid Atoms Solvent Atoms 159 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing