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Crystal structure of P. furiosus Mre11 DNA synaptic complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1II7 PDB ENTRY 1II7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 20% PEG 1000, 0.1 M Tris-HCl, 0.2 M MgCl2, 0.2 M 1,6 hexanediol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.13 42.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.477 α = 90 b = 106.071 β = 90 c = 76.667 γ = 90
Symmetry Space Group C 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 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 2.7 20 94.5 0.085 17.6 4.8 10769 1 1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 1II7 2.7 19.94 10769 9708 545 95.55 0.23034 0.23034 0.22756 0.2283 0.27804 0.2725 RANDOM 42.368
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] -1.71 4.77 -3.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.481 r_dihedral_angle_4_deg 16.295 r_dihedral_angle_3_deg 16.059 r_dihedral_angle_1_deg 4.865 r_angle_refined_deg 0.983 r_mcangle_it 0.354 r_nbtor_refined 0.31 r_symmetry_hbond_refined 0.238 r_mcbond_it 0.199 r_xyhbond_nbd_refined 0.152
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.481 r_dihedral_angle_4_deg 16.295 r_dihedral_angle_3_deg 16.059 r_dihedral_angle_1_deg 4.865 r_angle_refined_deg 0.983 r_mcangle_it 0.354 r_nbtor_refined 0.31 r_symmetry_hbond_refined 0.238 r_mcbond_it 0.199 r_xyhbond_nbd_refined 0.152 r_nbd_refined 0.146 r_symmetry_vdw_refined 0.129 r_scangle_it 0.099 r_chiral_restr 0.072 r_scbond_it 0.06 r_bond_refined_d 0.005 r_gen_planes_refined 0.002 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2754 Nucleic Acid Atoms 348 Solvent Atoms 63 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing