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Crystal structure of CBP bromodomain liganded with Y08175
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4NYX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.2M MgCl2 0.1M TrsHCl 30% PEG4000 PH7.5
Crystal Properties Matthews coefficient Solvent content 2.31 46.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.89 α = 90 b = 56.89 β = 90 c = 80.62 γ = 120
Symmetry Space Group P 31 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 197 PIXEL DECTRIS PILATUS3 6M 2018-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97736 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 1.82 80.62 100 0.067 0.073 0.027 0.997 17.9 7.2 14087
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 1.82 1.86 100 0.244 0.262 0.094 0.983 7.5
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 4NYX 1.82 49.27 13263 793 99.96 0.1946 0.193 0.2006 0.2209 0.2252 RANDOM 27.716
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] 0.64 0.32 0.64 -2.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.757 r_dihedral_angle_4_deg 12.465 r_dihedral_angle_3_deg 12.365 r_dihedral_angle_1_deg 4.996 r_angle_refined_deg 1.479 r_angle_other_deg 0.977 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.757 r_dihedral_angle_4_deg 12.465 r_dihedral_angle_3_deg 12.365 r_dihedral_angle_1_deg 4.996 r_angle_refined_deg 1.479 r_angle_other_deg 0.977 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1103 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms 49
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction MOLREP phasing