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Tetrahydroprotoberberine N-methyltransferase in complex with boldine 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 6.75 293 26% pentaerythritol ethoxylate, 15 mM ammonium sulfate, 0.1M Tris-Cl, 0.5 mM boldine, 0.5 mM SAM, 5% glycerol
Crystal Properties Matthews coefficient Solvent content 2.94 58.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.02 α = 90 b = 104.02 β = 90 c = 82.597 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 1.8 39.544 99.91 0.016 1 14.84 12.9 48088
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 1.8 1.83 100 0.437 0.697 1.14 11.5
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 1.8 39.544 48088 2460 99.917 0.169 0.1681 0.1688 0.1869 0.1872 RANDOM 36.251
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] 0.114 0.057 0.114 -0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.665 r_dihedral_angle_6_deg 12.321 r_lrange_it 11.19 r_scangle_it 9.544 r_scbond_it 7.139 r_dihedral_angle_1_deg 5.959 r_mcangle_it 5.582 r_dihedral_angle_2_deg 5.153 r_mcbond_it 4.742 r_angle_refined_deg 1.416
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.665 r_dihedral_angle_6_deg 12.321 r_lrange_it 11.19 r_scangle_it 9.544 r_scbond_it 7.139 r_dihedral_angle_1_deg 5.959 r_mcangle_it 5.582 r_dihedral_angle_2_deg 5.153 r_mcbond_it 4.742 r_angle_refined_deg 1.416 r_nbtor_refined 0.307 r_symmetry_xyhbond_nbd_refined 0.229 r_nbd_refined 0.221 r_symmetry_nbd_refined 0.195 r_xyhbond_nbd_refined 0.189 r_chiral_restr 0.092 r_gen_planes_refined 0.006 r_bond_refined_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2697 Nucleic Acid Atoms Solvent Atoms 358 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing