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Crystal Structure of Meganuclease I-SmaMI Bound to Uncleaveable DNA with a TTCT Central Four
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LOX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 25% PEG 3550, 5mM CaCl2
Crystal Properties Matthews coefficient Solvent content 2.42 49.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.869 α = 90 b = 179.282 β = 95.48 c = 65.401 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 100 CCD ADSC QUANTUM 315r 2015-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.55 ALS 5.0.2
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 3.1 50 98.5 0.221 0.229 0.061 5.1 13.8 16992
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 3.1 3.21 95.5 0.719 0.755 0.22 0.872 10.9 1666
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 4LOX 3.2 89.64 14881 784 98.84 0.2401 0.2377 0.2431 0.2861 0.2887 RANDOM 44.818
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] -3.32 -4.79 -2.44 6.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.345 r_dihedral_angle_3_deg 17.686 r_dihedral_angle_4_deg 14.072 r_dihedral_angle_1_deg 5.972 r_mcangle_it 4.89 r_mcbond_it 2.971 r_mcbond_other 2.97 r_angle_refined_deg 1.407 r_angle_other_deg 1.318 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.345 r_dihedral_angle_3_deg 17.686 r_dihedral_angle_4_deg 14.072 r_dihedral_angle_1_deg 5.972 r_mcangle_it 4.89 r_mcbond_it 2.971 r_mcbond_other 2.97 r_angle_refined_deg 1.407 r_angle_other_deg 1.318 r_chiral_restr 0.085 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4335 Nucleic Acid Atoms 2214 Solvent Atoms 4 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction Coot model building PHASER phasing HKL-2000 data reduction