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Tetrahydroprotoberberine N-methyltransferase in complex with (R)-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 0.1 M Tris-Cl, 15 mM ammonium sulfate, 29% pentaerythritol ethoxylate (15/4 EO/OH), 5% glycerol, 0.5 mM SAM, 0.5 mM R-reticuline
Crystal Properties Matthews coefficient Solvent content 2.95 58.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.013 α = 90 b = 104.013 β = 90 c = 82.863 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 37.641 98.36 0.044 0.996 10.31 3.4 34747
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 2.05 99.81 0.139 0.939 4.78 3.1
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2 37.641 34747 1783 98.344 0.149 0.1463 0.1482 0.1906 0.1907 RANDOM 28.469
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] 0.061 0.031 0.061 -0.198
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 14.003 r_dihedral_angle_6_deg 12.291 r_dihedral_angle_3_deg 11.282 r_scangle_it 10.46 r_scbond_it 7.512 r_dihedral_angle_1_deg 5.923 r_mcangle_it 5.73 r_mcbond_it 4.618 r_dihedral_angle_2_deg 3.166 r_angle_refined_deg 1.379
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 14.003 r_dihedral_angle_6_deg 12.291 r_dihedral_angle_3_deg 11.282 r_scangle_it 10.46 r_scbond_it 7.512 r_dihedral_angle_1_deg 5.923 r_mcangle_it 5.73 r_mcbond_it 4.618 r_dihedral_angle_2_deg 3.166 r_angle_refined_deg 1.379 r_nbtor_refined 0.306 r_symmetry_nbd_refined 0.21 r_nbd_refined 0.208 r_xyhbond_nbd_refined 0.208 r_symmetry_xyhbond_nbd_refined 0.197 r_chiral_restr 0.096 r_gen_planes_refined 0.006 r_bond_refined_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2696 Nucleic Acid Atoms Solvent Atoms 390 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing