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Crystal structure of SGF29 tandem tudor domain in complex with a Carba containing peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ME9 PDB entry 3ME9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 291 25% PEG3350, 0.1 M ammonium sulfate, 0.1 M Bis-Tris, pH 5.5
Crystal Properties Matthews coefficient Solvent content 1.98 37.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.109 α = 90 b = 65.193 β = 90 c = 105.217 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RIGAKU SATURN A200 2013-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54184
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 1.6 37.17 99.1 0.073 0.03 0.999 17.6 6.8 45670
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 92.1 0.775 0.32 0.766 2.6 6.6 2080
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 THROUGHOUT PDB entry 3ME9 1.6 37.17 44342 1269 98.89 0.205 0.204 0.2125 0.2391 0.2464 RANDOM 17.246
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] 0.04 -1.08 1.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.29 r_dihedral_angle_4_deg 18.339 r_dihedral_angle_3_deg 13.428 r_dihedral_angle_1_deg 7.55 r_mcangle_it 1.642 r_angle_refined_deg 1.384 r_mcbond_it 0.975 r_mcbond_other 0.974 r_angle_other_deg 0.916 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.29 r_dihedral_angle_4_deg 18.339 r_dihedral_angle_3_deg 13.428 r_dihedral_angle_1_deg 7.55 r_mcangle_it 1.642 r_angle_refined_deg 1.384 r_mcbond_it 0.975 r_mcbond_other 0.974 r_angle_other_deg 0.916 r_chiral_restr 0.085 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2811 Nucleic Acid Atoms Solvent Atoms 381 Heterogen Atoms 23
Software Software Software Name Purpose Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC refinement Coot model building