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H109K mutant of uracil DNA glycosylase X
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 2.03 45.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.45 α = 90 b = 51.75 β = 104.83 c = 54.63 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 2021-02-27 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 1.6 52.81 96.6 0.036 0.045 0.027 0.998 21.9 4.6 25154
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 1.6 1.63 65 0.119 0.161 0.107 0.966 5.5 2.9
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 THROUGHOUT 1.6 26.41 2 25132 1216 96.48 0.1648 0.1639 0.1667 0.1818 0.1933
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 5.777 f_angle_d 1.012 f_chiral_restr 0.064 f_plane_restr 0.009 f_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1508 Nucleic Acid Atoms Solvent Atoms 186 Heterogen Atoms 12
Software Software Software Name Purpose PHENIX refinement Aimless data scaling iMOSFLM data reduction PHASER phasing