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Crystal structure of CBP bromodomain liganded with CCS151
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 0.2M Sodium malonate pH 7.0, 20% w/v Polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.02 38.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.58 α = 90 b = 33.77 β = 94.66 c = 78.35 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 1.59 78.09 86.1 0.104 0.116 0.05 0.992 7.8 4.9 29393
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 1.59 1.62 95.7 0.449 0.504 0.224 0.858 4.8
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 1.59 78.09 27886 1480 85.59 0.1891 0.1869 0.1964 0.231 0.2359 RANDOM 22.583
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] -0.07 -0.44 -0.26 0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.365 r_dihedral_angle_4_deg 25.554 r_dihedral_angle_3_deg 15.431 r_dihedral_angle_1_deg 5.529 r_angle_refined_deg 1.895 r_angle_other_deg 1.308 r_chiral_restr 0.163 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_bond_other_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.365 r_dihedral_angle_4_deg 25.554 r_dihedral_angle_3_deg 15.431 r_dihedral_angle_1_deg 5.529 r_angle_refined_deg 1.895 r_angle_other_deg 1.308 r_chiral_restr 0.163 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_bond_other_d 0.005 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1940 Nucleic Acid Atoms Solvent Atoms 163 Heterogen Atoms 86
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction MOLREP phasing