6P3N

Tetrahydroprotoberberine N-methyltransferase in complex with S-adenosylmethionine


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7298S-adenosyl methionine, pentaerythritol ethoxylate (15/4 EO/OH), Glycerol, Ammonium sulfate, Tris-Cl
Crystal Properties
Matthews coefficientSolvent content
2.957.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 104.023α = 90
b = 104.023β = 90
c = 82.746γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-01-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-20.9800SSRLBL12-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.639.5698.90.0670.0750.99811.595.468160
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.6494.10.5360.5960.7995

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5KOK1.639.5664394346999.290.178680.177750.1957RANDOM31.489
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]
0.070.030.07-0.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.244
r_dihedral_angle_4_deg15.404
r_dihedral_angle_3_deg12.326
r_long_range_B_refined8.057
r_dihedral_angle_1_deg5.466
r_mcangle_it3.408
r_scbond_it3.353
r_mcbond_it2.254
r_angle_refined_deg1.151
r_chiral_restr0.078
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.244
r_dihedral_angle_4_deg15.404
r_dihedral_angle_3_deg12.326
r_long_range_B_refined8.057
r_dihedral_angle_1_deg5.466
r_mcangle_it3.408
r_scbond_it3.353
r_mcbond_it2.254
r_angle_refined_deg1.151
r_chiral_restr0.078
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2711
Nucleic Acid Atoms
Solvent Atoms414
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing