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Crystal structure of human TDRD1 extended Tudor domain in complex with a symmetrically dimethylated E2F peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4B9X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293.15 30% PEG4000, 0.2M MgCl2, 0.1 M Tris pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.26 45.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.91 α = 64.94 b = 52.962 β = 88.85 c = 59.619 γ = 67.67
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 2014-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 1.0282 Diamond I04
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 1.95 29.34 96.9 0.034 0.025 16.7 3.5 30788 33.712
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 1.99 89.8 0.411 2.3 3.5
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 4B9X 1.95 29.34 29186 1600 96.91 0.21482 0.21222 0.2179 0.26035 0.2633 RANDOM 44.441
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] -0.57 1.66 0.06 -3.11 0.17 3.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.716 r_dihedral_angle_3_deg 14.718 r_dihedral_angle_4_deg 12.824 r_dihedral_angle_1_deg 7.763 r_long_range_B_refined 6.133 r_long_range_B_other 6.127 r_mcangle_other 2.407 r_mcangle_it 2.406 r_scangle_other 2.325 r_angle_refined_deg 1.849
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.716 r_dihedral_angle_3_deg 14.718 r_dihedral_angle_4_deg 12.824 r_dihedral_angle_1_deg 7.763 r_long_range_B_refined 6.133 r_long_range_B_other 6.127 r_mcangle_other 2.407 r_mcangle_it 2.406 r_scangle_other 2.325 r_angle_refined_deg 1.849 r_mcbond_it 1.427 r_mcbond_other 1.424 r_scbond_it 1.409 r_scbond_other 1.409 r_angle_other_deg 0.969 r_chiral_restr 0.101 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3132 Nucleic Acid Atoms Solvent Atoms 79 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing