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Crystal structure of CBP bromodomain liganded with Y08092(31g)
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 20% PEG3350 0.2M KSCN 0.1M HEPES PH8.5
Crystal Properties Matthews coefficient Solvent content 2.2 44.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.119 α = 90 b = 75.309 β = 90 c = 123.489 γ = 90
Symmetry Space Group C 2 2 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 2018-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97906 SSRF BL19U1
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 2.35 61.74 83.8 0.161 0.186 0.091 0.967 5.5 3.6 9981
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 2.35 2.43 78.5 0.558 0.643 0.311 0.748 3.5
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 2.35 61.74 9484 478 82.84 0.1938 0.1913 0.1974 0.2419 0.2476 RANDOM 32.441
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] -0.53 1.74 -1.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.629 r_dihedral_angle_4_deg 17.758 r_dihedral_angle_3_deg 15.343 r_dihedral_angle_1_deg 6.036 r_angle_refined_deg 1.601 r_angle_other_deg 1.251 r_chiral_restr 0.082 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.629 r_dihedral_angle_4_deg 17.758 r_dihedral_angle_3_deg 15.343 r_dihedral_angle_1_deg 6.036 r_angle_refined_deg 1.601 r_angle_other_deg 1.251 r_chiral_restr 0.082 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1900 Nucleic Acid Atoms Solvent Atoms 46 Heterogen Atoms 77
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction MOLREP phasing