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Bromodomain-containing protein 4 (BRD4) bromodomain 2 (BD2) complexed with YF3-126
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OUO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 290 0.2 M (NH4)2SO4, 0.1M Na cacodylate pH 6.5, 30% PEG 8000
Crystal Properties Matthews coefficient Solvent content 3.36 63.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.01 α = 90 b = 63.01 β = 90 c = 102.722 γ = 120
Symmetry Space Group P 31 2 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 DECTRIS EIGER X 9M 2020-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.12713 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) 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 2.49 54.57 99.7 0.079 0.084 0.028 16.3 9.1 8677
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.49 2.59 99.9 0.442 0.466 0.147 4.9 9.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2OUO 2.49 54.57 8193 452 99.6 0.1816 0.18 0.2121 0.2181 RANDOM 50.905
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] 1.14 0.57 1.14 -3.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.468 r_dihedral_angle_4_deg 22.747 r_dihedral_angle_3_deg 17.287 r_dihedral_angle_1_deg 5.419 r_angle_refined_deg 1.683 r_angle_other_deg 1.343 r_chiral_restr 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.468 r_dihedral_angle_4_deg 22.747 r_dihedral_angle_3_deg 17.287 r_dihedral_angle_1_deg 5.419 r_angle_refined_deg 1.683 r_angle_other_deg 1.343 r_chiral_restr 0.087 r_bond_refined_d 0.012 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 905 Nucleic Acid Atoms Solvent Atoms 34 Heterogen Atoms 54
Software Software Software Name Purpose MOSFLM data reduction Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction MOLREP phasing