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Crystal Structure of the second bromodomain of human BRD2 in complex with the inhibitor Y13120
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6E6J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.2 M Lithium sulfate monohydrate, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.61 52.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.63 α = 90 b = 106.63 β = 90 c = 87.97 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 197 PIXEL DECTRIS PILATUS3 6M 2020-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97892 SSRF BL19U1
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 2.6 106.63 98.8 0.126 0.141 0.061 0.992 7.9 5 30036
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 2.6 2.72 100 0.67 0.747 0.325 0.692 5.3
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 6E6J 2.6 106.63 28466 1562 98.67 0.2116 0.2085 0.2155 0.2683 0.2648 RANDOM 56.596
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] 1.54 1.54 -3.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.961 r_dihedral_angle_4_deg 18.14 r_dihedral_angle_3_deg 18.097 r_dihedral_angle_1_deg 6.085 r_angle_refined_deg 1.694 r_angle_other_deg 1.029 r_chiral_restr 0.086 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.961 r_dihedral_angle_4_deg 18.14 r_dihedral_angle_3_deg 18.097 r_dihedral_angle_1_deg 6.085 r_angle_refined_deg 1.694 r_angle_other_deg 1.029 r_chiral_restr 0.086 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5369 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms 292
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction MOLREP phasing