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Complex form of MsmUdgX H109A mutant and uracil- obtained from uracil DNA (ttUtt) post its cleavage by UdgX H109A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6AJS H109S mutant of MsmUdgX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 7 295 2.0M Ammonium citrate tribasic pH7.0, 0.1M BIS-TRIS propane pH7.0
Crystal Properties Matthews coefficient Solvent content 2.11 41.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.71 α = 90 b = 50.72 β = 104.5 c = 55.06 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 IMAGE PLATE MAR scanner 345 mm plate 2021-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.54179
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 2.3 29.11 100 0.14 0.19 0.13 0.982 5.6 3.8 8832
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 100 0.43 0.59 0.39 0.753 2.4 3.7
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 THROUGHOUT 2.3 26.65 1.94 8820 428 100 0.1877 0.1858 0.1983 0.2222 0.2211
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 5.375 f_angle_d 0.61 f_chiral_restr 0.043 f_plane_restr 0.006 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1490 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms 16
Software Software Software Name Purpose PHENIX refinement Aimless data scaling iMOSFLM data reduction PHASER phasing