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Crystal structure of the first bromodomain (BD1) of human BRD4 (BRD4-1) in complex with bivalent inhibitor NC-III-49-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7K6H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.01 M Iron(III) chloride hexahydrate, 0.1 M Sodium citrate tribasic dihydrate (pH 5.6), 10% v/v Jeffamine M-600
Crystal Properties Matthews coefficient Solvent content 3.94 68.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.126 α = 90 b = 114.126 β = 90 c = 94.834 γ = 120
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 RIGAKU SATURN 944+ 2018-09-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5417
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.2 98.84 100 0.059 0.065 0.028 0.999 18.2 5.7 139185
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.25 100 2.649 2.93 1.248 0.435 5.5
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 7K6H 2.2 37.36 1.96 139185 4004 99.26 0.1853 0.1846 0.187 0.2077 0.2086 62.8059
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 10.569 f_angle_d 1.041 f_chiral_restr 0.056 f_bond_d 0.009 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5313 Nucleic Acid Atoms Solvent Atoms 268 Heterogen Atoms 255
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing