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First bromodomain of BRD4 bound to inhibitor XD47
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 PEG3350, succinic acid
Crystal Properties Matthews coefficient Solvent content 2.16 43.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.44 α = 90 b = 42.73 β = 90 c = 79.5 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 CCD RIGAKU SATURN 944+ 2013-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 1.83 13.2 99.1 0.07 11.1 3.6 12248
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 1.82 1.92 96.5 0.333 2.7 1712
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 1.93 13.2 9284 1006 99.43 0.17172 0.16854 0.1805 0.20136 0.2077 RANDOM 23.137
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] 0.93 -1.14 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.479 r_dihedral_angle_4_deg 26.889 r_dihedral_angle_3_deg 14.312 r_dihedral_angle_1_deg 5.597 r_long_range_B_refined 4.318 r_long_range_B_other 3.939 r_angle_refined_deg 1.325 r_scangle_other 1.051 r_mcangle_other 0.993 r_mcangle_it 0.991
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.479 r_dihedral_angle_4_deg 26.889 r_dihedral_angle_3_deg 14.312 r_dihedral_angle_1_deg 5.597 r_long_range_B_refined 4.318 r_long_range_B_other 3.939 r_angle_refined_deg 1.325 r_scangle_other 1.051 r_mcangle_other 0.993 r_mcangle_it 0.991 r_angle_other_deg 0.763 r_scbond_it 0.655 r_scbond_other 0.638 r_mcbond_it 0.582 r_mcbond_other 0.576 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.004 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 1062 Nucleic Acid Atoms Solvent Atoms 197 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PHASER phasing iMOSFLM data reduction