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Rieske non-heme iron monooxygenase for guaiacol O-demethylation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold Alphafold model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 1.0 M Ammonium citrate tribasic,
0.1 M Bistris propane
Crystal Properties Matthews coefficient Solvent content 4.78 74.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 315.58 α = 90 b = 315.58 β = 90 c = 189.962 γ = 120
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 EIGER2 XE 16M 2021-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97628 Diamond I03
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 3.71 157.79 88.05 0.398 0.418 0.127 0.989 1.2 10.1 65629
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 3.713 3.932 100 1.988 2.094 0.65 0.373 1.436 10.08
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 Alphafold model 3.712 157.79 65628 3290 88.05 0.176 0.1744 0.1776 0.2159 0.2146 RANDOM 133.211
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] -5.161 -5.161 10.322
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.336 r_lrange_it 25.357 r_lrange_other 25.357 r_mcangle_it 21.032 r_mcangle_other 21.032 r_scangle_it 20.601 r_scangle_other 20.6 r_dihedral_angle_3_deg 18.287 r_dihedral_angle_4_deg 17.042 r_mcbond_it 14.177
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.336 r_lrange_it 25.357 r_lrange_other 25.357 r_mcangle_it 21.032 r_mcangle_other 21.032 r_scangle_it 20.601 r_scangle_other 20.6 r_dihedral_angle_3_deg 18.287 r_dihedral_angle_4_deg 17.042 r_mcbond_it 14.177 r_mcbond_other 14.177 r_scbond_it 13.695 r_scbond_other 13.681 r_dihedral_angle_1_deg 8.779 r_angle_refined_deg 1.734 r_angle_other_deg 1.165 r_symmetry_xyhbond_nbd_refined 0.334 r_symmetry_nbd_refined 0.194 r_nbd_refined 0.182 r_nbd_other 0.153 r_nbtor_refined 0.15 r_metal_ion_refined 0.146 r_symmetry_nbd_other 0.138 r_symmetry_xyhbond_nbd_other 0.134 r_xyhbond_nbd_refined 0.114 r_ncsr_local_group_11 0.081 r_ncsr_local_group_17 0.08 r_ncsr_local_group_4 0.079 r_ncsr_local_group_16 0.079 r_ncsr_local_group_12 0.078 r_chiral_restr 0.077 r_ncsr_local_group_1 0.077 r_ncsr_local_group_15 0.077 r_ncsr_local_group_22 0.077 r_ncsr_local_group_2 0.076 r_ncsr_local_group_9 0.076 r_ncsr_local_group_18 0.076 r_ncsr_local_group_21 0.076 r_ncsr_local_group_5 0.074 r_ncsr_local_group_20 0.074 r_ncsr_local_group_27 0.074 r_symmetry_nbtor_other 0.073 r_ncsr_local_group_14 0.073 r_ncsr_local_group_28 0.073 r_ncsr_local_group_29 0.073 r_ncsr_local_group_7 0.072 r_ncsr_local_group_13 0.072 r_ncsr_local_group_30 0.072 r_ncsr_local_group_3 0.071 r_ncsr_local_group_10 0.071 r_ncsr_local_group_33 0.071 r_ncsr_local_group_8 0.07 r_ncsr_local_group_23 0.07 r_ncsr_local_group_26 0.07 r_ncsr_local_group_6 0.069 r_ncsr_local_group_24 0.069 r_ncsr_local_group_32 0.068 r_ncsr_local_group_19 0.067 r_ncsr_local_group_25 0.067 r_ncsr_local_group_31 0.066 r_ncsr_local_group_36 0.064 r_ncsr_local_group_35 0.063 r_ncsr_local_group_34 0.053 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 25280 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction STARANISO data scaling MOLREP phasing