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Crystal structure of the CBP bromodomain in complex with CPI703
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DWY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 277 0.1 M BICINE:NaOH pH 9.0, 20% (w/v) PEG 6000 (CPI703)
Crystal Properties Matthews coefficient Solvent content 2.56 51.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.588 α = 90 b = 34.034 β = 103.93 c = 117.727 γ = 90
Symmetry Space Group C 1 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 2015-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.9786 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.85 50 99.7 0.094 0.111 0.058 7.2 3.6 36503
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.92 99 0.68 0.803 0.422 0.674 3.5 3598
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 3DWY 1.86 50 34687 1816 99.41 0.1746 0.1723 0.1822 0.2202 0.2273 RANDOM 24.308
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] -0.19 -1.3 0.54 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.661 r_dihedral_angle_4_deg 15.273 r_dihedral_angle_3_deg 14.086 r_dihedral_angle_1_deg 5.947 r_angle_refined_deg 1.987 r_mcangle_it 1.688 r_mcbond_it 1.099 r_mcbond_other 1.082 r_angle_other_deg 0.963 r_chiral_restr 0.106
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.661 r_dihedral_angle_4_deg 15.273 r_dihedral_angle_3_deg 14.086 r_dihedral_angle_1_deg 5.947 r_angle_refined_deg 1.987 r_mcangle_it 1.688 r_mcbond_it 1.099 r_mcbond_other 1.082 r_angle_other_deg 0.963 r_chiral_restr 0.106 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2901 Nucleic Acid Atoms Solvent Atoms 357 Heterogen Atoms 66
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing