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Crystal Structure of BRD4 Bromodomain BD1 in Complex with Small Molecule PLX-3618
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other previously determined structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.1 293 0.2 M ammonium sulfate, 0.10 M Tris/HCl pH 8.10, 35.00% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.32 46.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.198 α = 90 b = 115.853 β = 90.119 c = 39.045 γ = 90
Symmetry Space Group P 1 21 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 Bruker PHOTON III 2021-03-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 LIQUID ANODE Excillum MetalJet D2+ 70 kV 1.34138
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 1.661 23.863 98.4 0.093 0.11 0.057 0.996 8.4 3.4 31041
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 1.661 1.721 93.6 0.431 0.542 0.322 0.652 2.2 2.5
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 MOLECULAR REPLACEMENT FREE R-VALUE 1.661 23.863 31040 1507 97.921 0.153 0.1501 0.1649 0.2017 0.2051 16.485
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] -4.332 -3.598 7.668 -3.336
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.264 r_dihedral_angle_4_deg 19.445 r_dihedral_angle_3_deg 14.573 r_dihedral_angle_1_deg 7.138 r_lrange_it 4.411 r_lrange_other 4.305 r_scangle_it 2.845 r_scangle_other 2.844 r_mcangle_it 2.427 r_mcangle_other 2.426
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.264 r_dihedral_angle_4_deg 19.445 r_dihedral_angle_3_deg 14.573 r_dihedral_angle_1_deg 7.138 r_lrange_it 4.411 r_lrange_other 4.305 r_scangle_it 2.845 r_scangle_other 2.844 r_mcangle_it 2.427 r_mcangle_other 2.426 r_angle_refined_deg 2.19 r_scbond_it 1.945 r_scbond_other 1.944 r_mcbond_it 1.713 r_mcbond_other 1.712 r_angle_other_deg 1.359 r_xyhbond_nbd_refined 0.229 r_nbd_refined 0.221 r_symmetry_xyhbond_nbd_refined 0.2 r_symmetry_nbd_other 0.194 r_nbtor_refined 0.189 r_nbd_other 0.184 r_symmetry_nbd_refined 0.147 r_symmetry_xyhbond_nbd_other 0.135 r_chiral_restr 0.095 r_symmetry_nbtor_other 0.081 r_bond_refined_d 0.017 r_gen_planes_refined 0.016 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2072 Nucleic Acid Atoms Solvent Atoms 292 Heterogen Atoms 140
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing