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BRD4-BD1 bound with compound 40
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5XHY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 7 289 10mg/ml, 2.8-3.8M sodium formate, glycerol 10%
Crystal Properties Matthews coefficient Solvent content 2.28 46.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.808 α = 90 b = 45.972 β = 90 c = 77.494 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 CCD ADSC QUANTUM 315r 2019-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.9723 SSRF BL17U1
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 1.759 39.54 97.5 0.184 0.982 11.7 10.7 25039 18.3814901972
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 1.759 1.85 0.628
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 5XHY 1.75909502055 23.3201371057 1.32597676106 25039 2530 96.6756756757 0.195640865434 0.191168855831 0.1909 0.235120276444 0.2336 SF FILE CONTAINS FRIEDEL PAIRS UNDER I_MINUS AND I_PLUS COLUMNS. 26.8866981733
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 17.2164891056 f_angle_d 1.09873394099 f_chiral_restr 0.0488588217446 f_bond_d 0.0103428695669 f_plane_restr 0.0070904336678
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1037 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 33
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing