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DNA binding and cleavage by the GIY-YIG endonuclease R.Eco29KI inactive variant E142Q
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Apo R.Eco29KI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 0.1M HEPES sodium, 0.8M sodium phosphate monobasic, 0.8M potassium phosphate monobasic, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.56 51.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.855 α = 90 b = 101.463 β = 110.19 c = 144.403 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 170 CCD RIGAKU SATURN 944 2010-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 2.5 135.53 99.5 0.064 19.31 6.6 93336 88621
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) 2.5 2.59 100 0.264 6.35 6.5
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 Apo R.Eco29KI 2.5 50 93336 88621 4677 99.5 0.21408 0.21089 0.2189 0.27368 0.2751 RANDOM 56.567
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] -0.99 3.36 -2.49 5.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.779 r_dihedral_angle_3_deg 20.84 r_dihedral_angle_4_deg 17.765 r_dihedral_angle_1_deg 7.39 r_scangle_it 3.251 r_scbond_it 2.161 r_angle_refined_deg 2.101 r_mcangle_it 1.69 r_mcbond_it 0.897 r_chiral_restr 0.132
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.779 r_dihedral_angle_3_deg 20.84 r_dihedral_angle_4_deg 17.765 r_dihedral_angle_1_deg 7.39 r_scangle_it 3.251 r_scbond_it 2.161 r_angle_refined_deg 2.101 r_mcangle_it 1.69 r_mcbond_it 0.897 r_chiral_restr 0.132 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13305 Nucleic Acid Atoms 3608 Solvent Atoms 493 Heterogen Atoms
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling