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O-methyltransferase from Desulfuromonas acetoxidans
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 291 0.1M MES/Imidazole pH6.5; 0.03M MgCl2 0.03M CaCl2; 16% Glycerol; 8% PEG4000
Crystal Properties Matthews coefficient Solvent content 2.26 45.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.791 α = 90 b = 44.791 β = 90 c = 204.919 γ = 90
Symmetry Space Group P 43 21 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 2022-10-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.0332 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 44.79 99.9 0.043 1 23 11.1 34799
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 0.227 0.963
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.5 43.796 34687 1706 99.842 0.174 0.1714 0.173 0.2173 0.2188 32.4
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] 0.427 0.427 -0.854
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.748 r_dihedral_angle_4_deg 15.418 r_dihedral_angle_3_deg 12.96 r_dihedral_angle_1_deg 6.132 r_rigid_bond_restr 4.348 r_scangle_it 4.032 r_scangle_other 4.03 r_lrange_it 3.944 r_lrange_other 3.939 r_scbond_it 3.578
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.748 r_dihedral_angle_4_deg 15.418 r_dihedral_angle_3_deg 12.96 r_dihedral_angle_1_deg 6.132 r_rigid_bond_restr 4.348 r_scangle_it 4.032 r_scangle_other 4.03 r_lrange_it 3.944 r_lrange_other 3.939 r_scbond_it 3.578 r_scbond_other 3.575 r_mcangle_other 3.131 r_mcangle_it 3.126 r_mcbond_it 2.681 r_mcbond_other 2.648 r_angle_refined_deg 1.773 r_angle_other_deg 1.508 r_nbd_other 0.287 r_symmetry_nbd_refined 0.257 r_nbd_refined 0.226 r_symmetry_nbd_other 0.183 r_nbtor_refined 0.167 r_xyhbond_nbd_refined 0.132 r_symmetry_xyhbond_nbd_refined 0.126 r_chiral_restr 0.097 r_symmetry_nbtor_other 0.087 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1449 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement Aimless data scaling Aimless data scaling MOLREP phasing XDS data reduction