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Structural basis of sequence-specific recruitment of histone deacetylases by Myocyte Enhancer Factor-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EGW PDB ENTRY 1EGW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 298 PEG 3500, sodium cholride, BTP, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.67 53.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.14 α = 90 b = 70.14 β = 90 c = 151.88 γ = 90
Symmetry Space Group P 41 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 101 CCD ADSC QUANTUM 4 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C APS 14-BM-C
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 2.2 30 90 0.059 38 19.5 18733 18733 23.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.28 54 0.059 0.37 4.4 4.4 1135
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 (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 PDB ENTRY 1EGW 2.2 28.99 17987 17987 1752 89.9 0.243 0.243 0.2785 0.268 0.3019 RANDOM 53.6
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] 5.32 5.32 -10.63
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 19.6 c_scangle_it 3.2 c_mcangle_it 2.73 c_scbond_it 2.46 c_mcbond_it 1.69 c_angle_deg 1.1 c_improper_angle_d 1.02 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1705 Nucleic Acid Atoms 568 Solvent Atoms 228 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement CNS phasing