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Ultra-high resolution crystal structure of second bromodomain of BRD2 in complex with inhibitor 6B3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2E3K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 300 30% PEG MME 2000, 50mM Tris-HCl pH 7.5, 50mM NaCl, 20% glycerol
Crystal Properties Matthews coefficient Solvent content 2.22 44.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32 α = 90 b = 52.37 β = 90 c = 71.46 γ = 90
Symmetry Space Group P 2 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 CCD MARMOSAIC 225 mm CCD 2015-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.7293 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 0.91 42.22 99.4 0.054 0.054 0.999 11.6 4.4 86054 7.031
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 0.91 0.96 100 1.627 0.9 4.1
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 2E3k 0.91 20 81790 4328 99.16 0.1262 0.12526 0.1344 0.14336 0.1507 RANDOM 12.231
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] 0.17 0.06 -0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.68 r_sphericity_free 26.73 r_dihedral_angle_4_deg 21.56 r_dihedral_angle_3_deg 12.673 r_sphericity_bonded 7.999 r_dihedral_angle_1_deg 4.866 r_rigid_bond_restr 3.674 r_angle_refined_deg 1.812 r_angle_other_deg 0.947 r_chiral_restr 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.68 r_sphericity_free 26.73 r_dihedral_angle_4_deg 21.56 r_dihedral_angle_3_deg 12.673 r_sphericity_bonded 7.999 r_dihedral_angle_1_deg 4.866 r_rigid_bond_restr 3.674 r_angle_refined_deg 1.812 r_angle_other_deg 0.947 r_chiral_restr 0.11 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 r_gen_planes_other 0.007 r_bond_other_d 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 945 Nucleic Acid Atoms Solvent Atoms 213 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PHASER phasing PDB_EXTRACT data extraction MOSFLM data reduction