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Tetrahydroprotoberberine N-methyltransferase E204A 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 5% glycerol, 0.1 M Tris-Cl, 0.5 mM SAM, 0.5 mM (S)-reticuline, 15 mM ammonium sulfate, 29% pentaerythritol ethoxylate (15/4 EO/OH)
Crystal Properties Matthews coefficient Solvent content 2.95 58.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.098 α = 90 b = 104.098 β = 90 c = 82.196 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 2020-07-03 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) R Sym 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 2.2 39.523 99.77 0.025 0.999 13.31 6.7 26423 35.83
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 2.28 99.65 0.127 0.949 4.23 6.5
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 2.2 39.523 26421 1362 99.773 0.167 0.166 0.1662 0.1963 0.1963 51.674
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] -0.053 -0.026 -0.053 0.171
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 15.073 r_scangle_it 14.77 r_dihedral_angle_3_deg 13.628 r_dihedral_angle_6_deg 12.446 r_scbond_it 12.345 r_mcangle_it 9.55 r_mcbond_it 8.154 r_dihedral_angle_1_deg 6.117 r_dihedral_angle_2_deg 5.43 r_angle_refined_deg 1.4
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 15.073 r_scangle_it 14.77 r_dihedral_angle_3_deg 13.628 r_dihedral_angle_6_deg 12.446 r_scbond_it 12.345 r_mcangle_it 9.55 r_mcbond_it 8.154 r_dihedral_angle_1_deg 6.117 r_dihedral_angle_2_deg 5.43 r_angle_refined_deg 1.4 r_nbtor_refined 0.305 r_nbd_refined 0.202 r_symmetry_nbd_refined 0.198 r_xyhbond_nbd_refined 0.177 r_symmetry_xyhbond_nbd_refined 0.173 r_chiral_restr 0.1 r_gen_planes_refined 0.006 r_bond_refined_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2693 Nucleic Acid Atoms Solvent Atoms 217 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing