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Crystal Structure of LAGLIDADG Meganuclease I-AabMI Bound to Uncleaved DNA
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, SITTING DROP 7.5 298 25% PEG 550 MME, 20mM CaCl2
Crystal Properties Matthews coefficient Solvent content 2.27 45.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.96 α = 97.18 b = 61.536 β = 99.1 c = 88.621 γ = 101.89
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 RIGAKU SATURN 944+ 2014-08-01 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 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 3.13 50 96.8 0.101 7.8 3.8 14205
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 3.13 3.24 91.2 0.324 3.4 1355
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 3QQY 3.24 50 12412 651 97.28 0.229 0.2253 0.2285 0.2988 0.2997 RANDOM 48.001
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] -0.33 1.51 0.99 -3.8 2.81 1.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.844 r_dihedral_angle_3_deg 20.665 r_dihedral_angle_4_deg 16.871 r_dihedral_angle_1_deg 6.655 r_mcangle_it 4.315 r_mcbond_it 2.588 r_mcbond_other 2.583 r_angle_other_deg 1.564 r_angle_refined_deg 1.385 r_chiral_restr 0.081
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.844 r_dihedral_angle_3_deg 20.665 r_dihedral_angle_4_deg 16.871 r_dihedral_angle_1_deg 6.655 r_mcangle_it 4.315 r_mcbond_it 2.588 r_mcbond_other 2.583 r_angle_other_deg 1.564 r_angle_refined_deg 1.385 r_chiral_restr 0.081 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4129 Nucleic Acid Atoms 2009 Solvent Atoms 19 Heterogen Atoms 5
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction Coot model building PHASER phasing