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The crystal structure of SHD931 in complex with Brd4-BD2 and VCB
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5T35
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 1500 mM Ammonium sulfate, 100 mM Tris base/ Hydrochloric acid, pH 8.5, 12% (v/v) Glycerol
Crystal Properties Matthews coefficient Solvent content 2.85 56.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.061 α = 90 b = 84.388 β = 90 c = 382.717 γ = 90
Symmetry Space Group C 2 2 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 PIXEL DECTRIS EIGER X 16M 2024-01-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL10U2 0.97918 SSRF BL10U2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.95 47.84 99.41 0.16 0.994 10.55 5.2 29155 72.98
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.95 3.055 1.085 0.615 1.85
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5T35 2.95 47.84 1.34 29096 2004 99.44 0.2417 0.2396 0.2413 0.2702 0.2716 76.51
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 12.5026 f_angle_d 0.6235 f_chiral_restr 0.0452 f_plane_restr 0.0043 f_bond_d 0.0042
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6992 Nucleic Acid Atoms Solvent Atoms 13 Heterogen Atoms 148
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing