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Crystal structure of BRD2(BD1)with ligand ZB-BD-224 bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YEK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 25-30% PEG MME 5000, 0.2M ammonium sulfate, 0.1M MES pH 6.7
Crystal Properties Matthews coefficient Solvent content 2.5 50.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.784 α = 90 b = 55.778 β = 94.245 c = 68.098 γ = 90
Symmetry Space Group C 1 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 DECTRIS PILATUS3 S 6M 2019-05-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.98 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.79 46 99.51 0.168 0.168 0.168 0.069 0.941 99.6 6.7 39802 33.5503799568
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.86 0.791 0.791 0.861 0.985 0.691
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 THROUGHOUT 2YEK 1.79998842375 45.4540515771 1.35505875512 39793 1974 99.5198199325 0.189761132575 0.188228271041 0.1912 0.218792906413 0.222 39.3003794775
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 11.7974546419 f_angle_d 0.903941093113 f_chiral_restr 0.0460961591378 f_bond_d 0.00673167430505 f_plane_restr 0.00542449894625
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2738 Nucleic Acid Atoms Solvent Atoms 214 Heterogen Atoms 72
Software Software Software Name Purpose PHENIX refinement HKL-3000 data reduction Aimless data scaling PHASER phasing