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O-Methyltransferase Plu4890 (mutant H229N) in complex with SAH and AQ-256
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8BGT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 0.2 M Sodium nitrate, 0.1 M bis-tris propane pH 6.5, 20 % PEG3350
Crystal Properties Matthews coefficient Solvent content 2.81 56.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.35 α = 90 b = 77.59 β = 95.27 c = 167.6 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 2020-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 48 97.9 0.079 8.5 3 107159
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.1 99 0.506 2.4
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 (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 8BGT 2 30 101773 5356 97.86 0.1734 0.1715 0.1822 0.2097 0.218 RANDOM 37.052
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] 0.81 0.78 1.34 -2.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.473 r_dihedral_angle_4_deg 16.628 r_dihedral_angle_3_deg 13.34 r_dihedral_angle_1_deg 5.918 r_angle_refined_deg 1.14 r_angle_other_deg 1.117 r_rigid_bond_restr 0.414 r_chiral_restr 0.042 r_gen_planes_refined 0.003 r_bond_refined_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.473 r_dihedral_angle_4_deg 16.628 r_dihedral_angle_3_deg 13.34 r_dihedral_angle_1_deg 5.918 r_angle_refined_deg 1.14 r_angle_other_deg 1.117 r_rigid_bond_restr 0.414 r_chiral_restr 0.042 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10288 Nucleic Acid Atoms Solvent Atoms 563 Heterogen Atoms 223
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing