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Crystal structure of the fifth bromodomain of human PB1 in complex with 1-ethylisochromeno[3,4-c]pyrazol-5(2H)-one) compound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3G0J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 0.1 M tris-sodium citrate dihydrate pH 5.6, 20% isopropanol, 20% PEG4K
Crystal Properties Matthews coefficient Solvent content 2.88 57.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.817 α = 90 b = 140.272 β = 90 c = 41.553 γ = 90
Symmetry Space Group C 2 2 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 DECTRIS PILATUS3 6M 2014-01-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9796 Diamond I03
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 1.7 28.91 99.3 0.043 0.023 28.2 7.8 19011 19011
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 1.7 1.73 89.7 0.36 3.9 4.2
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 3G0J 1.7 28.91 18059 941 99.21 0.1793 0.1778 0.1888 0.2076 0.2132 RANDOM 26.867
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] 1.38 -1.45 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.809 r_dihedral_angle_4_deg 12.942 r_dihedral_angle_3_deg 12.175 r_long_range_B_refined 7.036 r_long_range_B_other 7.033 r_scangle_other 5.261 r_dihedral_angle_1_deg 5.087 r_scbond_it 3.28 r_scbond_other 3.278 r_mcangle_it 2.747
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.809 r_dihedral_angle_4_deg 12.942 r_dihedral_angle_3_deg 12.175 r_long_range_B_refined 7.036 r_long_range_B_other 7.033 r_scangle_other 5.261 r_dihedral_angle_1_deg 5.087 r_scbond_it 3.28 r_scbond_other 3.278 r_mcangle_it 2.747 r_mcangle_other 2.745 r_mcbond_other 1.859 r_mcbond_it 1.858 r_angle_refined_deg 1.554 r_angle_other_deg 1.008 r_chiral_restr 0.097 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.003 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 957 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing