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DNA binding and cleavage by the GIY-YIG endonuclease R.Eco29kI inactive variant Y49F
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other DNA-bound-L69K-E142Q-R.Eco29kI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 298 0.1 M sodium acetate trihydrate, 2M ammonium sulphate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.53 51.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.87 α = 90 b = 101.346 β = 109.59 c = 142.346 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 110 CCD ADSC QUANTUM 315 2010-05-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 1.0 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.8 50 99.5 0.106 18.69 7.4 65980 62596 13.44
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.8 2.87 97.7 0.345 4.36 6.9 6405
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT DNA-bound-L69K-E142Q-R.Eco29kI 2.8 50 65980 62596 3347 99.5 0.20996 0.20641 0.2126 0.27856 0.2857 RANDOM 46.075
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] -3.1 0.61 -3.51 7.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.971 r_dihedral_angle_3_deg 19.836 r_dihedral_angle_4_deg 18.813 r_dihedral_angle_1_deg 7.224 r_scangle_it 2.486 r_angle_refined_deg 1.971 r_scbond_it 1.547 r_mcangle_it 1.223 r_mcbond_it 0.64 r_chiral_restr 0.112
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.971 r_dihedral_angle_3_deg 19.836 r_dihedral_angle_4_deg 18.813 r_dihedral_angle_1_deg 7.224 r_scangle_it 2.486 r_angle_refined_deg 1.971 r_scbond_it 1.547 r_mcangle_it 1.223 r_mcbond_it 0.64 r_chiral_restr 0.112 r_bond_refined_d 0.016 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13150 Nucleic Acid Atoms 3608 Solvent Atoms 466 Heterogen Atoms 55
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling