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Crystal Structure of the first bromodomain of human BRD4 BD1 in complex with the inhibitor Y13221
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7WJS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 1.0 M Sodium phosphate monobasic monohydrate, Potassium phosphate dibasic / pH 8.2
Crystal Properties Matthews coefficient Solvent content 3.88 68.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.067 α = 90 b = 142.067 β = 90 c = 134.141 γ = 120
Symmetry Space Group P 61 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS PILATUS 6M 2024-01-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.97918 SSRF BL02U1
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 3 123.03 100 0.167 0.172 0.039 0.998 12.4 18.8 16573
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 3 3.18 100 1.53 1.571 0.352 0.882 19.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 THROUGHOUT 7WJS 3 123.03 15660 863 99.88 0.20962 0.20655 0.2135 0.26451 0.261 RANDOM 92.681
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] -4.75 -2.38 -4.75 15.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.399 r_dihedral_angle_3_deg 19.779 r_long_range_B_other 12.354 r_long_range_B_refined 12.352 r_dihedral_angle_4_deg 11.982 r_scangle_other 8.679 r_mcangle_other 8.391 r_mcangle_it 8.389 r_dihedral_angle_1_deg 6.351 r_mcbond_it 5.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.399 r_dihedral_angle_3_deg 19.779 r_long_range_B_other 12.354 r_long_range_B_refined 12.352 r_dihedral_angle_4_deg 11.982 r_scangle_other 8.679 r_mcangle_other 8.391 r_mcangle_it 8.389 r_dihedral_angle_1_deg 6.351 r_mcbond_it 5.309 r_scbond_it 5.289 r_scbond_other 5.289 r_mcbond_other 5.284 r_angle_refined_deg 1.472 r_angle_other_deg 1.107 r_chiral_restr 0.055 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2732 Nucleic Acid Atoms Solvent Atoms 2 Heterogen Atoms 123
Software Software Software Name Purpose REFMAC refinement Aimless data scaling xia2 data reduction MOLREP phasing