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Structure of Sda1 nuclease with bound zinc ion
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 8 296 2.5uL of protein (26.7mg/mL) was mixed with 3.5uL of 90mM imidazole pH 8, 0.18M zinc acetate, 18% (w/v) PEG3000
Crystal Properties Matthews coefficient Solvent content 1.67 26.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.104 α = 108.72 b = 66.538 β = 90.01 c = 83.536 γ = 92.36
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93.15 CCD RIGAKU SATURN 944 2015-08-10 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 Sym 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 1.95 50 97.1 0.092 16.45 4.5 73933 73933
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) 1 1.95 1.98 88.4 0.325 2.91 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.95 33.132 1.98 73913 1923 96.52 0.2161 0.215 0.2601 0.2929 random selection
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 12.025 f_angle_d 0.978 f_chiral_restr 0.04 f_bond_d 0.007 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7478 Nucleic Acid Atoms Solvent Atoms 428 Heterogen Atoms 69
Software Software Software Name Purpose PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing