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The crystal structure of BRD4-BD1 in complex with inhibitor 39b
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7EHW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 0.2M potassium tartrate, 20%PEG3350, 0.1M Bis Tris, pH7.0
Crystal Properties Matthews coefficient Solvent content 2.14 42.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.667 α = 90 b = 43.829 β = 90 c = 77.674 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 PIXEL DECTRIS PILATUS 6M 2023-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97853 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.5 38.84 99.1 0.999 31.2 10.3 21082
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 0.983
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.5 38.84 1.36 21032 2000 98.95 0.1764 0.1743 0.1749 0.1965 0.1972
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 13.854 f_angle_d 0.842 f_chiral_restr 0.041 f_plane_restr 0.007 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1046 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms 55
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing