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Structure of the transposase domain of human Histone-lysine N-methyltransferase SETMAR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2F7T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 Purified SETMAR transposase domain was crystallized in 20% PEG 3350, 0.2 M di-Na Tartrate., pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.11 41.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 158.826 α = 90 b = 46.521 β = 92.04 c = 61.748 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 200 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E DW 1.504
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.85 36815 36815
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 2F7T 1.85 79.31 34969 1846 94.59 0.20764 0.20494 0.2036 0.25617 0.2562 RANDOM 28.035
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] -0.14 0.49 0.24 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.091 r_dihedral_angle_4_deg 21.307 r_dihedral_angle_3_deg 12.709 r_dihedral_angle_1_deg 5.741 r_scangle_it 4.056 r_scbond_it 2.907 r_mcangle_it 1.853 r_angle_refined_deg 1.729 r_mcbond_it 1.254 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.091 r_dihedral_angle_4_deg 21.307 r_dihedral_angle_3_deg 12.709 r_dihedral_angle_1_deg 5.741 r_scangle_it 4.056 r_scbond_it 2.907 r_mcangle_it 1.853 r_angle_refined_deg 1.729 r_mcbond_it 1.254 r_nbtor_refined 0.308 r_symmetry_hbond_refined 0.223 r_nbd_refined 0.212 r_xyhbond_nbd_refined 0.193 r_symmetry_vdw_refined 0.165 r_chiral_restr 0.129 r_bond_refined_d 0.022 r_gen_planes_refined 0.009 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 3127 Nucleic Acid Atoms Solvent Atoms 406 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction