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Crystal structure of CBP bromodomain liganded with Y08284
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 0.2 M Magnesium acetate tetrahydrate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 20% w/v Polyethylene glycol 8,000
Crystal Properties Matthews coefficient Solvent content 2.29 46.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.385 α = 90 b = 63.267 β = 90 c = 97.288 γ = 90
Symmetry Space Group P 21 21 21
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 2.17 53.04 99.8 0.064 0.068 0.022 0.999 17.7 9.2 16053
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 2.17 2.24 99.9 0.935 0.989 0.317 0.868 9.5
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 2.17 53.04 15233 785 99.65 0.2018 0.1989 0.2103 0.2587 0.2566 RANDOM 54.822
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] 0.84 -3.05 2.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.735 r_dihedral_angle_4_deg 20.066 r_dihedral_angle_3_deg 15.831 r_dihedral_angle_1_deg 5.826 r_angle_refined_deg 1.625 r_angle_other_deg 1.069 r_chiral_restr 0.086 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.735 r_dihedral_angle_4_deg 20.066 r_dihedral_angle_3_deg 15.831 r_dihedral_angle_1_deg 5.826 r_angle_refined_deg 1.625 r_angle_other_deg 1.069 r_chiral_restr 0.086 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.004 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1926 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 76
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing