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First bromodomain of BRD4 bound to inhibitor XD42
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 PEG3350, Bis-tris, sodium chloride
Crystal Properties Matthews coefficient Solvent content 1.87 34.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.43 α = 90 b = 47.46 β = 90 c = 57.51 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+ 2012-12-21 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 2.2 15.3 99.2 0.149 6.2 3.4 6065
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 2.2 2.32 99.7 0.451 2.6 869
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 2.2 15.3 5460 584 98.73 0.21787 0.21519 0.2172 0.24302 0.2472 RANDOM 24.352
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] -0.49 2.21 -1.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.608 r_dihedral_angle_4_deg 17.163 r_dihedral_angle_3_deg 17.017 r_dihedral_angle_1_deg 4.414 r_long_range_B_refined 1.8 r_long_range_B_other 1.667 r_angle_refined_deg 1.199 r_angle_other_deg 0.766 r_scangle_other 0.653 r_scbond_it 0.354
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.608 r_dihedral_angle_4_deg 17.163 r_dihedral_angle_3_deg 17.017 r_dihedral_angle_1_deg 4.414 r_long_range_B_refined 1.8 r_long_range_B_other 1.667 r_angle_refined_deg 1.199 r_angle_other_deg 0.766 r_scangle_other 0.653 r_scbond_it 0.354 r_scbond_other 0.354 r_mcangle_it 0.272 r_mcangle_other 0.272 r_mcbond_it 0.148 r_mcbond_other 0.148 r_chiral_restr 0.052 r_bond_refined_d 0.006 r_bond_other_d 0.004 r_gen_planes_refined 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 65 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PHASER phasing iMOSFLM data reduction