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Crystal structure of human SND1 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 3OMC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293.15 10 % PEG 1000, 10% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.27 45.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.243 α = 90 b = 80.626 β = 90.38 c = 39.289 γ = 90
Symmetry Space Group P 1 21 1
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 2015-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 1.45 28.14 96 0.037 16.2 3.8 38367
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 1.45 1.48 69.9 0.292 2.8 2.8
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 3OMC 1.45 28.14 36421 1920 95.83 0.23039 0.22892 0.2347 0.2612 0.2687 RANDOM 21.625
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] 0.53 -0.42 -0.05 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.344 r_dihedral_angle_4_deg 18.25 r_dihedral_angle_3_deg 12.276 r_dihedral_angle_1_deg 8.439 r_long_range_B_refined 4.759 r_long_range_B_other 4.596 r_scangle_other 2.628 r_mcangle_it 2.196 r_mcangle_other 2.195 r_scbond_it 1.634
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.344 r_dihedral_angle_4_deg 18.25 r_dihedral_angle_3_deg 12.276 r_dihedral_angle_1_deg 8.439 r_long_range_B_refined 4.759 r_long_range_B_other 4.596 r_scangle_other 2.628 r_mcangle_it 2.196 r_mcangle_other 2.195 r_scbond_it 1.634 r_scbond_other 1.633 r_angle_refined_deg 1.539 r_mcbond_other 1.365 r_mcbond_it 1.364 r_angle_other_deg 0.959 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 1752 Nucleic Acid Atoms Solvent Atoms 166 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing