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Crystal Structure of SMAD5-MH1 in complex with a composite DNA sequence
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KMP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 0.1M Bis-tris, pH 6.5, 0.2M LiNO3, 8% PEG 3350, 5% glycerol
Crystal Properties Matthews coefficient Solvent content 3.98 69.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.464 α = 90 b = 119.464 β = 90 c = 93.067 γ = 120
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 ADSC QUANTUM 315r 2014-11-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.979065 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 3.2 40 98.8 0.095 0.046 22.11 5.5 24244
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 3.2 3.31 100 0.556 0.257 0.929 4.55 5.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE 3KMP 3.2 29.937 1.96 24146 1234 98.68 0.2125 0.2105 0.2117 0.2526 0.2531 Random 125.1
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 23.136 f_angle_d 1.231 f_chiral_restr 0.069 f_bond_d 0.011 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3575 Nucleic Acid Atoms 1804 Solvent Atoms Heterogen Atoms 4
Software Software Software Name Purpose PHENIX refinement HKL-2000 data collection HKL-2000 data scaling PHASER phasing