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Tetrahydroprotoberberine N-methyltransferase E207A mutant in complex with (S)-reticuline and SAM
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6P3O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 26% pentaerythritol ethoxylate (15/4 EO/OH), 15 mM ammonium sulfate, 0.1 M Tris-Cl, 7.5% glycerol, 0.5 mM (S)-reticuline, 0.5 mM SAM
Crystal Properties Matthews coefficient Solvent content 2.94 58.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.989 α = 90 b = 103.989 β = 90 c = 82.444 γ = 120
Symmetry Space Group P 32 2 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 PILATUS 6M 2020-11-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.9795 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2 39.52 99.88 1 0.023 14.1 35097
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 99.59 0.451 0.691 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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2 39.518 35097 1806 99.878 0.177 0.1749 0.1773 0.2081 0.2096 47.108
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] 0.024 0.012 0.024 -0.078
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 14.404 r_dihedral_angle_6_deg 13.527 r_dihedral_angle_3_deg 13.358 r_lrange_it 11.966 r_scangle_it 10.049 r_scbond_it 6.797 r_mcangle_it 6.047 r_dihedral_angle_1_deg 6.046 r_mcbond_it 4.362 r_angle_refined_deg 1.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 14.404 r_dihedral_angle_6_deg 13.527 r_dihedral_angle_3_deg 13.358 r_lrange_it 11.966 r_scangle_it 10.049 r_scbond_it 6.797 r_mcangle_it 6.047 r_dihedral_angle_1_deg 6.046 r_mcbond_it 4.362 r_angle_refined_deg 1.65 r_symmetry_nbd_refined 0.315 r_nbtor_refined 0.306 r_nbd_refined 0.207 r_xyhbond_nbd_refined 0.165 r_symmetry_xyhbond_nbd_refined 0.133 r_chiral_restr 0.108 r_bond_refined_d 0.008 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2721 Nucleic Acid Atoms Solvent Atoms 191 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing