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Crystal Structure of LAGLIDADG Meganuclease I-CpaMI 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, HANGING DROP 7.5 298 26% PEG 3350, 5mM DDT, 5mM CaCl2
Crystal Properties Matthews coefficient Solvent content 2.39 48.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.869 α = 90 b = 91.799 β = 90 c = 139.636 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 100 CCD RIGAKU SATURN 944+ 2014-05-06 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 2.8 50 94.2 0.101 13.3 3.2 23588
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 2.8 2.9 93.9 0.692 3 2308
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 2.89 50 20174 1065 94.3 0.2202 0.2173 0.2204 0.2737 0.2727 RANDOM 41.837
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] 3.58 -3.74 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.334 r_dihedral_angle_3_deg 17.962 r_dihedral_angle_4_deg 17.627 r_dihedral_angle_1_deg 6.308 r_mcangle_it 3.26 r_angle_other_deg 3.098 r_mcbond_it 2.195 r_mcbond_other 2.185 r_angle_refined_deg 1.253 r_chiral_restr 0.073
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.334 r_dihedral_angle_3_deg 17.962 r_dihedral_angle_4_deg 17.627 r_dihedral_angle_1_deg 6.308 r_mcangle_it 3.26 r_angle_other_deg 3.098 r_mcbond_it 2.195 r_mcbond_other 2.185 r_angle_refined_deg 1.253 r_chiral_restr 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_gen_planes_other 0.005 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4570 Nucleic Acid Atoms 2280 Solvent Atoms 37 Heterogen Atoms 25
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction Coot model building PHASER phasing