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Crystal structure of Dna2 nuclease-helicase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 80 mm MES pH 6.5, 250 mM Li2SO4, 8-12% PEG MME 5000, 2 mM MgCl2
Crystal Properties Matthews coefficient Solvent content 3.25 62.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.9 α = 90 b = 148.6 β = 90 c = 170.5 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 PIXEL DECTRIS PILATUS 6M 2012-02-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.987 APS 24-ID-C
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 50 98.3 0.131 0.149 0.068 4.1 4.4 61754
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 3.11 98.9 0.787 0.897 0.419 0.708 4.5 6133
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT 3 50 54064 1388 89.17 0.2102 0.2092 0.2468 0.2145 RANDOM 63.636
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] -1.08 -3.11 4.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.771 r_dihedral_angle_3_deg 20.946 r_dihedral_angle_4_deg 20.349 r_dihedral_angle_1_deg 7.55 r_mcangle_it 6.605 r_scbond_it 4.485 r_mcbond_it 3.982 r_angle_refined_deg 1.7 r_chiral_restr 0.119 r_bond_refined_d 0.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.771 r_dihedral_angle_3_deg 20.946 r_dihedral_angle_4_deg 20.349 r_dihedral_angle_1_deg 7.55 r_mcangle_it 6.605 r_scbond_it 4.485 r_mcbond_it 3.982 r_angle_refined_deg 1.7 r_chiral_restr 0.119 r_bond_refined_d 0.011 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16542 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PDB_EXTRACT data extraction HKL-2000 data reduction SHARP phasing