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Tetrahydroprotoberberine N-methyltransferase product complex with N-methyltetrahydropalmatine and SAH
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 29% pentaerythritol ethoxylate (15/4 EO/OH), 0.1 M Tris-Cl, 5% glycerol, 5 mM ammonium sulfate, 0.5mM SAM, 0.5mm tetrahydropalmatine
Crystal Properties Matthews coefficient Solvent content 2.96 58.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.982 α = 90 b = 103.982 β = 90 c = 82.989 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 1.85 37.69 99.38 0.036 0.998 10.63 5.7 44273
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 1.85 1.89 97.1 0.296 0.744 2.24 5.6
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 1.85 37.686 44271 2292 99.372 0.158 0.1562 0.1568 0.185 0.1861 30.101
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] 0.3 0.15 0.3 -0.974
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 12.802 r_dihedral_angle_3_deg 12.427 r_lrange_it 11.131 r_scangle_it 9.683 r_scbond_it 6.996 r_dihedral_angle_1_deg 5.767 r_mcangle_it 5.642 r_mcbond_it 4.218 r_dihedral_angle_2_deg 3.558 r_angle_refined_deg 1.283
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 12.802 r_dihedral_angle_3_deg 12.427 r_lrange_it 11.131 r_scangle_it 9.683 r_scbond_it 6.996 r_dihedral_angle_1_deg 5.767 r_mcangle_it 5.642 r_mcbond_it 4.218 r_dihedral_angle_2_deg 3.558 r_angle_refined_deg 1.283 r_nbtor_refined 0.305 r_symmetry_nbd_refined 0.271 r_symmetry_xyhbond_nbd_refined 0.21 r_nbd_refined 0.197 r_xyhbond_nbd_refined 0.19 r_chiral_restr 0.091 r_gen_planes_refined 0.006 r_bond_refined_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2730 Nucleic Acid Atoms Solvent Atoms 400 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing