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Crystal Structure of LAGLIDADG Meganuclease I-GpeMI 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 8.5 298 22.5% PEG 3000, 50mM CaCl2
Crystal Properties Matthews coefficient Solvent content 2.2 44.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.985 α = 90 b = 39.895 β = 90.43 c = 73.986 γ = 90
Symmetry Space Group C 1 2 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 2013-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.97 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 2.15 50 99.3 0.101 0.119 0.063 14.8 3.5 24373
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 2.15 2.23 97.6 0.455 0.547 0.301 0.794 3 2366
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 2.15 50 23084 1237 98.69 0.1812 0.1779 0.1857 0.244 0.246 RANDOM 36.192
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] -2.86 -1.18 1.01 1.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.686 r_dihedral_angle_4_deg 19.401 r_dihedral_angle_3_deg 15.118 r_dihedral_angle_1_deg 6.619 r_mcangle_it 3.757 r_mcbond_it 2.606 r_mcbond_other 2.591 r_angle_refined_deg 1.627 r_angle_other_deg 1.047 r_chiral_restr 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.686 r_dihedral_angle_4_deg 19.401 r_dihedral_angle_3_deg 15.118 r_dihedral_angle_1_deg 6.619 r_mcangle_it 3.757 r_mcbond_it 2.606 r_mcbond_other 2.591 r_angle_refined_deg 1.627 r_angle_other_deg 1.047 r_chiral_restr 0.09 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2310 Nucleic Acid Atoms 1101 Solvent Atoms 219 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction Coot model building PHASER phasing HKL-2000 data reduction