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Crystal structure of UbaLAI restriction endonuclease B3 domain domain (mutant L24M L53M L95M) with cognate DNA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 291 Crystallization buffer was 0.15 M Na-Citrate (pH 5.6), 20% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.39 48.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.775 α = 90 b = 94.583 β = 90 c = 123.403 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 PIXEL PSI PILATUS 6M 2012-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.82661 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.346 94.583 99.6 0.035 0.035 0.04 0.016 25.6 6.6 63722 21.07
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.69 99.7 0.443 0.443 0.515 0.196 1.8 6.7
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 SIRAS FREE R-VALUE 1.6 51.678 1.31 63634 12080 99.22 0.1624 0.1593 0.1694 0.1906 0.1974 29.4586
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 19.595 f_angle_d 1.771 f_chiral_restr 0.099 f_bond_d 0.019 f_plane_restr 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2516 Nucleic Acid Atoms 726 Solvent Atoms 419 Heterogen Atoms
Software Software Software Name Purpose SCALA data scaling SHELX phasing Coot model building PHENIX refinement PDB_EXTRACT data extraction XDS data reduction