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Crystal structure of anthocyanin 4'-O-methyltransferase from Vitis vinifera L.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8XE4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 10% v/v polyethylene glycol 200, 0.1 M Bis-Tris propane pH 9.0, 18% w/v polyethylene glycol 8000
Crystal Properties Matthews coefficient Solvent content 2.97 58.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.592 α = 90 b = 199.159 β = 101.67 c = 95.332 γ = 90
Symmetry Space Group P 1 21 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 PILATUS3 6M 2023-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.97918 SSRF BL02U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.78 99.58 97.6 0.148 0.167 0.075 0.985 7.1 4.7 60305
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 2.78 2.93 0.725 0.412
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FREE R-VALUE 2.78 46.68 1.38 59539 2980 96.39 0.2499 0.2469 0.2464 0.306 0.3034
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 12.52 f_angle_d 0.748 f_chiral_restr 0.045 f_plane_restr 0.005 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14264 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms 208
Software Software Software Name Purpose PHENIX refinement XDS data scaling PDB_EXTRACT data extraction XDS data reduction PHENIX phasing