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First bromodomain of BRD4 bound to inhibitor XD35
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 PEG3350, Bis-tris, ammonium acetate
Crystal Properties Matthews coefficient Solvent content 1.92 36.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.58 α = 90 b = 47.94 β = 90 c = 58.32 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 PIXEL PSI PILATUS 6M 2012-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.000 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.5 37 97.4 0.068 9.6 3.5 18613
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 1.5 1.58 98.3 0.183 2.4 2693
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.5 37 16718 1850 96.38 0.17881 0.17631 0.1761 0.20128 0.2011 RANDOM 16.011
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] 1.06 -1.42 0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.609 r_dihedral_angle_4_deg 26.865 r_dihedral_angle_3_deg 12.875 r_dihedral_angle_1_deg 4.809 r_long_range_B_refined 3.429 r_long_range_B_other 3.065 r_angle_refined_deg 1.362 r_angle_other_deg 0.791 r_scangle_other 0.545 r_mcangle_it 0.424
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.609 r_dihedral_angle_4_deg 26.865 r_dihedral_angle_3_deg 12.875 r_dihedral_angle_1_deg 4.809 r_long_range_B_refined 3.429 r_long_range_B_other 3.065 r_angle_refined_deg 1.362 r_angle_other_deg 0.791 r_scangle_other 0.545 r_mcangle_it 0.424 r_mcangle_other 0.424 r_scbond_it 0.345 r_scbond_other 0.344 r_mcbond_it 0.249 r_mcbond_other 0.248 r_chiral_restr 0.075 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.003 r_bond_other_d 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 1062 Nucleic Acid Atoms Solvent Atoms 195 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PHASER phasing iMOSFLM data reduction