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Crystal structure of the first bromodomain of human BRD4 bound to CPI-0610
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OSS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.8 277 3.4-3.8 M sodium formate, 0.1 M Tris pH 7.8, and 10% glycerol
Crystal Properties Matthews coefficient Solvent content 2.07 40.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.788 α = 90 b = 47.634 β = 90 c = 77.775 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 100 IMAGE PLATE RIGAKU RAXIS IV 2013-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.18 50 90 0.108 16.4 4.3 6289
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.18 2.26 70.2 0.25 8.5 3.2
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2OSS 2.182 40.62 5826 435 90.13 0.19204 0.18601 0.1942 0.27717 0.2788 RANDOM 23.785
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] 3.78 -2.66 -1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.198 r_dihedral_angle_4_deg 21.354 r_dihedral_angle_3_deg 17.774 r_dihedral_angle_1_deg 6.306 r_long_range_B_refined 5.164 r_long_range_B_other 5.011 r_scangle_other 3.455 r_mcangle_it 2.811 r_mcangle_other 2.811 r_scbond_it 2.334
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.198 r_dihedral_angle_4_deg 21.354 r_dihedral_angle_3_deg 17.774 r_dihedral_angle_1_deg 6.306 r_long_range_B_refined 5.164 r_long_range_B_other 5.011 r_scangle_other 3.455 r_mcangle_it 2.811 r_mcangle_other 2.811 r_scbond_it 2.334 r_scbond_other 2.307 r_mcbond_it 2.024 r_mcbond_other 2.02 r_angle_refined_deg 1.416 r_angle_other_deg 0.693 r_chiral_restr 0.084 r_gen_planes_refined 0.014 r_bond_refined_d 0.01 r_gen_planes_other 0.001 r_bond_other_d 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 1061 Nucleic Acid Atoms Solvent Atoms 153 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing