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CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX with compound 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MXF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.1M bis-tris-propane pH 7.9, 20% PEG3350, 0.2M sodium fluoride, 10% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.11 41.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.263 α = 90 b = 43.862 β = 90 c = 77.89 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 2018-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.915870 Diamond I04-1
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 1.226 38.945 98.2 0.0432 0.0475 0.0195 0.999 20.59 5.26 37506
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) 1.226 1.253 78.8 0.2418 0.3069 0.1851 0.888 3.57 2.16 1875
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE 1.226 38.945 37502 1872 98.224 0.119 0.1172 0.1315 0.1482 0.1551 8.133
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] -0.635 -0.084 0.718
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.472 r_dihedral_angle_6_deg 16.578 r_lrange_it 16.361 r_lrange_other 15.722 r_dihedral_angle_3_deg 11.38 r_scangle_it 6.739 r_scangle_other 6.736 r_dihedral_angle_1_deg 5.656 r_scbond_it 4.772 r_scbond_other 4.768
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.472 r_dihedral_angle_6_deg 16.578 r_lrange_it 16.361 r_lrange_other 15.722 r_dihedral_angle_3_deg 11.38 r_scangle_it 6.739 r_scangle_other 6.736 r_dihedral_angle_1_deg 5.656 r_scbond_it 4.772 r_scbond_other 4.768 r_mcangle_other 4.323 r_mcangle_it 4.307 r_rigid_bond_restr 4.131 r_mcbond_it 2.872 r_mcbond_other 2.783 r_angle_refined_deg 1.998 r_angle_other_deg 0.699 r_symmetry_nbd_refined 0.427 r_xyhbond_nbd_refined 0.307 r_symmetry_xyhbond_nbd_refined 0.284 r_nbd_refined 0.257 r_nbtor_refined 0.197 r_symmetry_nbd_other 0.175 r_nbd_other 0.158 r_metal_ion_refined 0.15 r_chiral_restr 0.113 r_symmetry_nbtor_other 0.08 r_symmetry_metal_ion_refined 0.07 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1059 Nucleic Acid Atoms Solvent Atoms 216 Heterogen Atoms 32
Software Software Software Name Purpose autoPROC data processing XDS data reduction Aimless data scaling STARANISO data scaling REFMAC refinement