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The structure of the UdgX mutant H109E at a pre-excision state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6IO9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 298 19% PEG3350, 0.1 M sodium citrate, 0.2 M NaCl
Crystal Properties Matthews coefficient Solvent content 2.14 42.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.698 α = 90 b = 48.316 β = 90 c = 86.222 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD OXFORD ONYX CCD 2019-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.8 21.56 98.1 0.064 0.998 15.9 4.8 18687 8.78342573865
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 1.8 1.9 95.1 0.128 0.985 8.4 4.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 6IO9 1.80007323734 21.55545 1.3379521463 18632 920 97.6366399413 0.153380596451 0.151306999552 0.1515 0.192672984964 0.1917 11.6844359257
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 18.4341084538 f_angle_d 1.66750134875 f_chiral_restr 0.0565940780818 f_bond_d 0.0121540859019 f_plane_restr 0.00594241724132
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1536 Nucleic Acid Atoms Solvent Atoms 268 Heterogen Atoms 20
Software Software Software Name Purpose PHENIX refinement CrysalisPro data reduction CrysalisPro data scaling PHASER phasing