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Structure of the bipartite DNA-binding domain of Tc3 transposase bound to transposon DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TC3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 Na acetate, glycerol, DTT, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.93 77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.681 α = 90 b = 93.681 β = 90 c = 255.558 γ = 120
Symmetry Space Group P 61 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 100 IMAGE PLATE MARRESEARCH 2001-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A 1.0749 EMBL/DESY, HAMBURG BW7A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.69 12 98.5 0.092 0.092 20 18091 17820 101
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.69 2.8 98.9 2
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 1TC3 2.69 12 18091 17820 954 98.55 0.23515 0.23515 0.23329 0.2859 0.27291 0.3181 RANDOM 20.441
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] -1.94 -0.97 -1.94 2.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.901 r_scangle_it 2.066 r_angle_refined_deg 1.897 r_scbond_it 1.388 r_mcangle_it 1.038 r_mcbond_it 0.557 r_symmetry_hbond_refined 0.246 r_nbd_refined 0.217 r_xyhbond_nbd_refined 0.197 r_symmetry_vdw_refined 0.182
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.901 r_scangle_it 2.066 r_angle_refined_deg 1.897 r_scbond_it 1.388 r_mcangle_it 1.038 r_mcbond_it 0.557 r_symmetry_hbond_refined 0.246 r_nbd_refined 0.217 r_xyhbond_nbd_refined 0.197 r_symmetry_vdw_refined 0.182 r_chiral_restr 0.098 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 816 Nucleic Acid Atoms 1060 Solvent Atoms 7 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction CCP4 data scaling AMoRE phasing