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Crystal Structure of the second bromodomain of human BRD2 in complex with the inhibitor 22
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7WNI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 60% v/v Tacsimate pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.74 67.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.782 α = 90 b = 95.497 β = 90 c = 109.08 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 80 PIXEL DECTRIS PILATUS3 6M 2023-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.97918 SSRF BL02U1
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 3.13 109.08 100 0.364 0.4 0.163 0.951 5.9 6 17520
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 3.13 3.35 100 0.726 0.794 0.317 0.717 6.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7wni 3.13 71.85 16542 931 99.93 0.19786 0.19452 0.25677 0.2231 RANDOM 51.416
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] 3.91 -1.4 -2.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.734 r_dihedral_angle_4_deg 19.549 r_dihedral_angle_3_deg 19.172 r_long_range_B_refined 8.694 r_long_range_B_other 8.693 r_scangle_other 6.142 r_dihedral_angle_1_deg 6.024 r_mcangle_it 5.121 r_mcangle_other 5.12 r_scbond_it 3.707
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.734 r_dihedral_angle_4_deg 19.549 r_dihedral_angle_3_deg 19.172 r_long_range_B_refined 8.694 r_long_range_B_other 8.693 r_scangle_other 6.142 r_dihedral_angle_1_deg 6.024 r_mcangle_it 5.121 r_mcangle_other 5.12 r_scbond_it 3.707 r_scbond_other 3.706 r_mcbond_it 3.163 r_mcbond_other 3.162 r_angle_refined_deg 1.764 r_angle_other_deg 1.123 r_chiral_restr 0.087 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3631 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms 160
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing