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Crystal structure of tea N9-methyltransferase CkTcS in complex with SAH and 1,3,7-trimethyluric acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EFJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 0.1 M HEPES (pH 7.5), 1 M Sodium Citrate
Crystal Properties Matthews coefficient Solvent content 2.93 57.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.744 α = 90.211 b = 86.812 β = 90.039 c = 123.258 γ = 90.172
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2019-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 1.0000 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.14 50 96.4 0.995 9.7 2.5 62167 62.383110248
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.15 3.2 1.11 0.845
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2EFJ 3.15000316024 43.8717918208 1.96340305611 62167 2254 99.8 0.263952027126 0.262661324434 0.2626 0.29805388409 0.307
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.7725512309 f_angle_d 0.830450179397 f_chiral_restr 0.0296365552682 f_plane_restr 0.00379874033725 f_bond_d 0.00373389999454
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20792 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement PHENIX refinement HKL-2000 data scaling PHENIX phasing Coot model building HKL-2000 data reduction