☰ Navigation Tabs
Tetrahydroprotoberberine N-methyltransferase product complex with dextromethorphan 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), 0.1 M Tris-Cl, 10 mM ammonium sulfate, 5% glycerol, 0.5 mM dextromethorphan, 0.5 mM SAM
Crystal Properties Matthews coefficient Solvent content 2.94 58.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.992 α = 90 b = 103.992 β = 90 c = 82.536 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 39.53 99.88 0.011 1 19.52 13.4 68044
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 99.7 0.312 0.791 1.98 13.4
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 39.53 68043 3480 99.877 0.172 0.1707 0.176 0.1912 0.1942 38.517
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] 0.088 0.044 0.088 -0.285
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 11.703 r_dihedral_angle_3_deg 11.37 r_lrange_it 10.291 r_scangle_it 8.356 r_scbond_it 5.771 r_dihedral_angle_1_deg 5.763 r_mcangle_it 5.059 r_mcbond_it 3.578 r_dihedral_angle_2_deg 2.817 r_angle_refined_deg 1.117
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 11.703 r_dihedral_angle_3_deg 11.37 r_lrange_it 10.291 r_scangle_it 8.356 r_scbond_it 5.771 r_dihedral_angle_1_deg 5.763 r_mcangle_it 5.059 r_mcbond_it 3.578 r_dihedral_angle_2_deg 2.817 r_angle_refined_deg 1.117 r_nbtor_refined 0.302 r_symmetry_xyhbond_nbd_refined 0.216 r_nbd_refined 0.19 r_symmetry_nbd_refined 0.186 r_xyhbond_nbd_refined 0.135 r_chiral_restr 0.089 r_gen_planes_refined 0.004 r_bond_refined_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2721 Nucleic Acid Atoms Solvent Atoms 343 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing