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Crystal structure of CBP bromodomain liganded with CCS1477
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5XXH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.1M HEPES pH 7.5, 2% v/v Tacsimate pH 7.0, 20% w/v Polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.01 38.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.457 α = 90 b = 33.713 β = 95.13 c = 78.342 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 197 PIXEL DECTRIS PILATUS3 6M 2021-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97915 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 78.03 98.8 0.054 0.059 0.023 0.999 15.9 6.5 25492
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 1.75 1.78 95.8 0.612 0.673 0.275 0.81 5.7
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 5XXH 1.75 78.03 24255 1225 98.52 0.1913 0.1895 0.1997 0.2265 0.2308 RANDOM 33.365
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] 0.5 -0.71 -1.3 0.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.206 r_dihedral_angle_4_deg 21.492 r_dihedral_angle_3_deg 15.814 r_dihedral_angle_1_deg 5.06 r_angle_refined_deg 1.672 r_angle_other_deg 1.168 r_chiral_restr 0.093 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.206 r_dihedral_angle_4_deg 21.492 r_dihedral_angle_3_deg 15.814 r_dihedral_angle_1_deg 5.06 r_angle_refined_deg 1.672 r_angle_other_deg 1.168 r_chiral_restr 0.093 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1874 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms 88
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing