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Crystal structure of the second bromodomain of human TAF1 in complex with BAY-299 chemical probe
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3UV4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277.15 20%PEG 10K, 0.20 M NaCl, 0.1M citrate/phosphate pH 4.2
Crystal Properties Matthews coefficient Solvent content 1.93 36.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.739 α = 90 b = 64.739 β = 90 c = 101.082 γ = 120
Symmetry Space Group P 31 2 1
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 DECTRIS PILATUS 6M 2016-01-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9794 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.75 101.08 96.3 0.061 0.035 17.3 7.4 24216
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 1.75 1.85 100 0.693 2.8 7.8 3618
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 3UV4 1.75 56.07 22959 1222 96.15 0.18796 0.18633 0.1854 0.22039 0.2156 RANDOM 41.255
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] -0.65 -0.65 -0.65 2.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.123 r_dihedral_angle_4_deg 29.974 r_sphericity_free 19.852 r_dihedral_angle_3_deg 14.757 r_sphericity_bonded 12.847 r_dihedral_angle_1_deg 4.603 r_rigid_bond_restr 3.538 r_angle_refined_deg 1.277 r_angle_other_deg 0.773 r_chiral_restr 0.068
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.123 r_dihedral_angle_4_deg 29.974 r_sphericity_free 19.852 r_dihedral_angle_3_deg 14.757 r_sphericity_bonded 12.847 r_dihedral_angle_1_deg 4.603 r_rigid_bond_restr 3.538 r_angle_refined_deg 1.277 r_angle_other_deg 0.773 r_chiral_restr 0.068 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001 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_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 1114 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing