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Tetrahydroprotoberberine N-methyltransferase complex with N-methylcanadine and SAH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6P30
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 33% Pentaerythritol ethoxylate (15/4 EO/OH) 0.1 mM Tris-Cl, 15% glycerol, 0.5 mM SAM, 0.5 mM canadine
Crystal Properties Matthews coefficient Solvent content 2.9 57.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.066 α = 90 b = 103.066 β = 90 c = 82.928 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 1.75 39.3 98.62 0.053 0.994 6.41 6.6 50909
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 1.75 1.78 0.388 0.749 1.46
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 1.75 39.299 50909 2612 98.688 0.165 0.1642 0.1693 0.1869 0.1915 33.317
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] 0.633 0.317 0.633 -2.054
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.721 r_dihedral_angle_3_deg 12.662 r_lrange_it 9.452 r_scangle_it 8.567 r_scbond_it 6.871 r_dihedral_angle_1_deg 6.289 r_mcangle_it 5.068 r_dihedral_angle_2_deg 4.856 r_mcbond_it 4.309 r_angle_refined_deg 1.322
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.721 r_dihedral_angle_3_deg 12.662 r_lrange_it 9.452 r_scangle_it 8.567 r_scbond_it 6.871 r_dihedral_angle_1_deg 6.289 r_mcangle_it 5.068 r_dihedral_angle_2_deg 4.856 r_mcbond_it 4.309 r_angle_refined_deg 1.322 r_nbtor_refined 0.309 r_symmetry_nbd_refined 0.289 r_nbd_refined 0.201 r_xyhbond_nbd_refined 0.168 r_symmetry_xyhbond_nbd_refined 0.151 r_chiral_restr 0.09 r_gen_planes_refined 0.006 r_bond_refined_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2787 Nucleic Acid Atoms Solvent Atoms 396 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing