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Structure of E2F8, an atypical member of E2F family of transcription factors
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CF7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.09 293 Hepes, PEG 4000, ammonium sulfate, PEG 400
Crystal Properties Matthews coefficient Solvent content 4.63 73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.83 α = 90 b = 98.83 β = 90 c = 121.69 γ = 120
Symmetry Space Group P 32 2 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 PSI PILATUS 6M 2013-05-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97628 ESRF ID23-1
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 3.073 49.591 97 0.169 8.67 6.5 77733 12768 123
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.07 3.182 89.2
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 THROUGHOUT 1CF7 3.073 14.918 2.02 12641 632 96.44 0.272 0.2716 0.3028 0.2968 0.3143 random 153.7
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 22.53 f_angle_d 0.661 f_chiral_restr 0.03 f_bond_d 0.003 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1515 Nucleic Acid Atoms 615 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose PHASER phasing PHENIX refinement XSCALE data scaling Coot model building XDS data reduction