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CorZ in complex with SAH and myxarylin, Methyltransferase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 291 15-34% precipitant mix 2 (40% v/v ethylene glycol; 20% w/v PEG 8000), 0.09M halogens (0.3M sodium fluoride; 0.3M sodium bromide; sodium iodide) and buffer system 3 pH 8 - 9 (tris(base); bicine)
Crystal Properties Matthews coefficient Solvent content 2.75 55.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.436 α = 90 b = 117.84 β = 100.2 c = 106.91 γ = 90
Symmetry Space Group I 1 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 EIGER X 16M 2022-04-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.0332 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.7 45.38 95.7 0.122 0.048 0.99 15.2 14.5 26746
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.83 1.084 0.428 0.835
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 2.7 45.38 1.34 26730 1375 95.49 0.2267 0.2243 0.2263 0.2697 0.2718
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 18.075 f_angle_d 0.709 f_chiral_restr 0.043 f_plane_restr 0.01 f_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6076 Nucleic Acid Atoms Solvent Atoms 61 Heterogen Atoms 174
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction XDS data reduction SCALA data scaling PHASER phasing