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Tetrahydroprotoberberine N-methyltransferase E207A mutant 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 26% Pentaerythritol ethoxylate (15/4 EO/OH), 15 mM ammonium sulfate, 6% Glycerol, 0.5 mM (R)-reticuline, 0.5 mM SAM, 0.1 mM Tris-Cl
Crystal Properties Matthews coefficient Solvent content 2.93 58.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.693 α = 90 b = 103.693 β = 90 c = 82.697 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 39.46 99.81 0.016 1 14.84 13.4 67813
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 1.62 100 0.44 0.698 1.14 13.7
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 39.459 67813 3468 99.863 0.179 0.1777 0.181 0.1958 0.1965 43.702
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] 0.019 0.009 0.019 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 12.537 r_lrange_it 11.591 r_dihedral_angle_3_deg 11.062 r_scangle_it 9.066 r_scbond_it 6.584 r_dihedral_angle_1_deg 5.833 r_mcangle_it 4.998 r_mcbond_it 3.913 r_dihedral_angle_2_deg 2.564 r_angle_refined_deg 1.165
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 12.537 r_lrange_it 11.591 r_dihedral_angle_3_deg 11.062 r_scangle_it 9.066 r_scbond_it 6.584 r_dihedral_angle_1_deg 5.833 r_mcangle_it 4.998 r_mcbond_it 3.913 r_dihedral_angle_2_deg 2.564 r_angle_refined_deg 1.165 r_nbtor_refined 0.303 r_symmetry_nbd_refined 0.209 r_nbd_refined 0.201 r_xyhbond_nbd_refined 0.173 r_symmetry_xyhbond_nbd_refined 0.159 r_chiral_restr 0.087 r_gen_planes_refined 0.005 r_bond_refined_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2693 Nucleic Acid Atoms Solvent Atoms 360 Heterogen Atoms 63
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing