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Crystal structure of LAGLIDADG homing endonuclease I-GzeII in complex with DNA target
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 298 30% PEG 6000
0.1M HEPES pH 7.5
2mM CaCl2
26bp duplex DNA with single base 3' overhang
Crystal Properties Matthews coefficient Solvent content 2.22 44.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.833 α = 90 b = 61.186 β = 116.3 c = 128.871 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 2011-06-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 0.999 ALS 5.0.2
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 2.8 115.526 98.7 0.091 22.9 6.5 20664
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) 2.8 2.9 90 0.34 2.8 4.1
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 2.8 50 20664 1113 98.66 0.1764 0.173 0.1775 0.2402 0.238 RANDOM 41.118
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] 1.65 -2.21 2.15 -1.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.305 r_dihedral_angle_3_deg 18.1 r_dihedral_angle_4_deg 16.862 r_dihedral_angle_1_deg 6.273 r_mcangle_it 2.877 r_mcbond_it 1.657 r_mcbond_other 1.652 r_angle_refined_deg 1.517 r_angle_other_deg 1.298 r_chiral_restr 0.087
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.305 r_dihedral_angle_3_deg 18.1 r_dihedral_angle_4_deg 16.862 r_dihedral_angle_1_deg 6.273 r_mcangle_it 2.877 r_mcbond_it 1.657 r_mcbond_other 1.652 r_angle_refined_deg 1.517 r_angle_other_deg 1.298 r_chiral_restr 0.087 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.004 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4603 Nucleic Acid Atoms 2170 Solvent Atoms 129 Heterogen Atoms 4
Software Software Software Name Purpose HKL-2000 data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction Coot model building