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Crystal structure of Dna2 in complex with a 5' overhang DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EAW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 80 mM MES, 20 mM CaCl2, 10 mM spermidine, 4-9 % isopropanol, 0.5 mM TCEP, pH 6.5, and 1 mM ADP
Crystal Properties Matthews coefficient Solvent content 3.13 60.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.153 α = 90 b = 118.488 β = 90 c = 149.26 γ = 90
Symmetry Space Group P 2 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 PSI PILATUS 6M 2014-07-21 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 2.35 50 99 0.126 0.142 0.063 5.3 5 63876
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 2.35 2.43 98.6 0.656 0.756 0.366 0.75 3.9 6265
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 5EAW 2.36 50 57871 1799 92.27 0.2094 0.2083 0.2121 0.246 0.2482 RANDOM 66.556
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] 5.72 -2.1 -3.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.534 r_dihedral_angle_4_deg 21.299 r_dihedral_angle_3_deg 18.871 r_dihedral_angle_1_deg 6.248 r_scbond_it 2.582 r_mcangle_it 2.365 r_angle_refined_deg 1.554 r_mcbond_it 1.498 r_chiral_restr 0.104 r_bond_refined_d 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.534 r_dihedral_angle_4_deg 21.299 r_dihedral_angle_3_deg 18.871 r_dihedral_angle_1_deg 6.248 r_scbond_it 2.582 r_mcangle_it 2.365 r_angle_refined_deg 1.554 r_mcbond_it 1.498 r_chiral_restr 0.104 r_bond_refined_d 0.01 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8302 Nucleic Acid Atoms 309 Solvent Atoms 4 Heterogen Atoms 37
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction SCALEPACK data scaling