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PglX methyltransferase from the Salmonella BREX phage defence system (aka BrxX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 15% PEG 3000 MME
0.1 M Tris pH 7.5
0.1 M Magnesium chloride
Crystal Properties Matthews coefficient Solvent content 3.46 64.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.539 α = 90 b = 138.539 β = 90 c = 407.956 γ = 90
Symmetry Space Group P 41 21 2
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 EIGER2 S 16M 2022-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 3.4 70.65 99.9 0.047 0.067 0.999 8 1.9 55797 159.62
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.4 3.5 99.4 1.515 2.142 0.214 1.9
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 3.5 61.72 1.33 55797 4289 87.42 0.2661 0.2653 0.2648 0.2805 0.2813 168.05
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 24.6908 f_angle_d 0.9115 f_chiral_restr 0.0509 f_plane_restr 0.0061 f_bond_d 0.0046
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19794 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 54
Software Software Software Name Purpose PHENIX refinement PHENIX refinement xia2.multiplex data reduction Aimless data scaling PHASER phasing