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Tetrahydroprotoberberine N-methyltransferase 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 6.75 293 15 mM ammonium sulfate, 26% pentaerythritol ethoxylate (15/4 EO/OH), 0.1 M Tris-Cl, 0.5 mM (S)-reticuline, 0.5 mM SAM, 5% glycerol
Crystal Properties Matthews coefficient Solvent content 2.95 58.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.033 α = 90 b = 104.033 β = 90 c = 82.704 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) 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 1.6 37.582 99.85 0.013 1 18.47 13.5 68219
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 1.6 1.62 97.12 0.724 0.451 0.85 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 1.6 37.582 68219 3492 99.845 0.176 0.1748 0.1803 0.1962 0.2 49.043
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] 0.027 0.013 0.027 -0.087
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 10.951 r_lrange_it 10.87 r_dihedral_angle_3_deg 10.848 r_scangle_it 8.87 r_scbond_it 5.887 r_dihedral_angle_1_deg 5.534 r_mcangle_it 5.069 r_mcbond_it 3.619 r_dihedral_angle_2_deg 2.384 r_angle_refined_deg 1.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 10.951 r_lrange_it 10.87 r_dihedral_angle_3_deg 10.848 r_scangle_it 8.87 r_scbond_it 5.887 r_dihedral_angle_1_deg 5.534 r_mcangle_it 5.069 r_mcbond_it 3.619 r_dihedral_angle_2_deg 2.384 r_angle_refined_deg 1.004 r_nbtor_refined 0.298 r_nbd_refined 0.189 r_symmetry_xyhbond_nbd_refined 0.189 r_symmetry_nbd_refined 0.16 r_xyhbond_nbd_refined 0.144 r_chiral_restr 0.081 r_gen_planes_refined 0.004 r_bond_refined_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2704 Nucleic Acid Atoms Solvent Atoms 304 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing