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Crystal Structure of the second bromodomain of human BRD4 BD2 in complex with the inhibitor Y13190
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6VIX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.01 M Iron(III) chloride hexahydrate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 10% v/v Jeffamine M-600
Crystal Properties Matthews coefficient Solvent content 3.08 60.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.913 α = 90 b = 125.108 β = 90.04 c = 300.352 γ = 90
Symmetry Space Group C 1 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 80 PIXEL DECTRIS PILATUS3 6M 2024-03-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97918 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 2.2 300.35 100 0.155 0.168 0.064 0.997 6 6.8 217025
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 2.2 2.24 100 2.487 2.7 1.04 0.286 6.7
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 6IVX 2.2 300.35 205956 10956 99.95 0.2572 0.25628 0.2591 0.27444 0.2763 RANDOM 65.457
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] -3.39 -0.06 -0.99 4.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.779 r_dihedral_angle_3_deg 19.476 r_dihedral_angle_4_deg 18.474 r_long_range_B_refined 7.339 r_long_range_B_other 7.339 r_dihedral_angle_1_deg 5.128 r_scangle_other 4.735 r_mcangle_it 4.561 r_mcangle_other 4.561 r_mcbond_it 2.769
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.779 r_dihedral_angle_3_deg 19.476 r_dihedral_angle_4_deg 18.474 r_long_range_B_refined 7.339 r_long_range_B_other 7.339 r_dihedral_angle_1_deg 5.128 r_scangle_other 4.735 r_mcangle_it 4.561 r_mcangle_other 4.561 r_mcbond_it 2.769 r_mcbond_other 2.768 r_scbond_it 2.748 r_scbond_other 2.748 r_angle_refined_deg 1.847 r_angle_other_deg 1.363 r_chiral_restr 0.203 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.003 r_gen_planes_other 0.001 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 17934 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms 986
Software Software Software Name Purpose REFMAC refinement Aimless data scaling DIALS data reduction MOLREP phasing