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Crystal Structure of the second bromodomain of human BRD2 in complex with the inhibitor Y13158
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 Sodium malonate pH 4.0, 20% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 3.77 67.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.685 α = 90 b = 108.685 β = 90 c = 81.58 γ = 90
Symmetry Space Group P 41 21 2
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 2021-05-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97915 SSRF BL18U1
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 3.12 76.85 99.9 0.301 0.332 0.136 0.798 4 5.5 9140
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 3.12 3.34 100 0.739 0.813 0.331 0.819 5.5
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 3.12 76.85 8654 461 99.75 0.2104 0.2078 0.2137 0.2575 0.2546 RANDOM 46.485
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] -5.34 -5.34 10.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.515 r_dihedral_angle_4_deg 23.79 r_dihedral_angle_3_deg 19.181 r_dihedral_angle_1_deg 6.227 r_angle_refined_deg 1.711 r_angle_other_deg 0.989 r_chiral_restr 0.073 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.515 r_dihedral_angle_4_deg 23.79 r_dihedral_angle_3_deg 19.181 r_dihedral_angle_1_deg 6.227 r_angle_refined_deg 1.711 r_angle_other_deg 0.989 r_chiral_restr 0.073 r_bond_refined_d 0.016 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 1802 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms 107
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction MOLREP phasing