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Bromodomain-containing protein 4 (BRD4) bromodomain 1 (BD1) complexed with XR844
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MXF PDB entry 3MXF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 289 1.6 M ammonium sulfate, 0.1 M HEPES, pH 7.5, 0.1 M sodium chloride
Crystal Properties Matthews coefficient Solvent content 2.42 49.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.158 α = 90 b = 42.303 β = 90 c = 90.557 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 EIGER X 9M 2021-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.0332 APS 21-ID-D
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 1.35 42.3 97 0.081 0.089 0.036 0.995 11.7 5.9 31930
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 1.35 1.37 77.5 0.363 0.438 0.239 0.832 3.2
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 PDB entry 3MXF 1.35 38.36 30290 1586 96.6 0.1702 0.1692 0.1791 0.1895 0.1921 RANDOM 17.917
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] 1.53 -0.74 -0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.848 r_dihedral_angle_4_deg 16.01 r_dihedral_angle_3_deg 14.13 r_dihedral_angle_1_deg 5.837 r_angle_refined_deg 1.954 r_angle_other_deg 1.478 r_chiral_restr 0.097 r_bond_refined_d 0.019 r_gen_planes_refined 0.013 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.848 r_dihedral_angle_4_deg 16.01 r_dihedral_angle_3_deg 14.13 r_dihedral_angle_1_deg 5.837 r_angle_refined_deg 1.954 r_angle_other_deg 1.478 r_chiral_restr 0.097 r_bond_refined_d 0.019 r_gen_planes_refined 0.013 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1065 Nucleic Acid Atoms Solvent Atoms 119 Heterogen Atoms 51
Software Software Software Name Purpose XDS data reduction Aimless data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction