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Intermediate engineered variant of I-OnuI meganuclease with improved thermostability and partially altered specificity
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QQY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 100mM sodium acetate pH 6.0, 200mM calcium acetate, 35% PEG 400
Crystal Properties Matthews coefficient Solvent content 1.86 33.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.288 α = 90 b = 62.586 β = 90 c = 157.405 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 108 PIXEL DECTRIS PILATUS3 6M 2019-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.977 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.85 50 99.7 0.035 0.037 0.011 20.2 11.3 33122
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.92 96.7 0.162 0.175 0.063 0.988 7.3
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 THROUGHOUT 3QQY 1.852 48.985 1.34 33033 1998 99.55 0.1935 0.1909 0.1934 0.2342 0.2347 29.35
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 17.022 f_angle_d 1.136 f_chiral_restr 0.062 f_bond_d 0.01 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2283 Nucleic Acid Atoms 1025 Solvent Atoms 139 Heterogen Atoms 4
Software Software Software Name Purpose SCALEPACK data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction DENZO data reduction