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Crystal Structure of bromodomain of human CBP in complex with the inhibitor CZL-046
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7XH6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.2 M Potassium sulfate, 20% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.24 45.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.379 α = 90 b = 60.637 β = 90 c = 61.177 γ = 90
Symmetry Space Group P 2 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 80 PIXEL DECTRIS PILATUS3 6M 2024-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.97918 SSRF BL02U1
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 2.67 61.18 99.6 0.162 0.178 0.073 0.992 9.3 5.8 4375
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 2.67 2.8 99.8 0.654 0.732 0.323 0.82 5.1
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 7XH6 2.67 43.07 4082 264 99.36 0.23803 0.23438 0.2382 0.28962 0.2927 RANDOM 39.397
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] -1.64 2.98 -1.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.845 r_dihedral_angle_4_deg 18.517 r_dihedral_angle_3_deg 18.111 r_dihedral_angle_1_deg 5.454 r_long_range_B_refined 3.995 r_long_range_B_other 3.994 r_scangle_other 2.497 r_mcangle_it 2.217 r_mcangle_other 2.215 r_scbond_it 1.436
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.845 r_dihedral_angle_4_deg 18.517 r_dihedral_angle_3_deg 18.111 r_dihedral_angle_1_deg 5.454 r_long_range_B_refined 3.995 r_long_range_B_other 3.994 r_scangle_other 2.497 r_mcangle_it 2.217 r_mcangle_other 2.215 r_scbond_it 1.436 r_scbond_other 1.434 r_mcbond_other 1.319 r_mcbond_it 1.318 r_angle_refined_deg 1.306 r_angle_other_deg 1.106 r_chiral_restr 0.051 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 998 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MERLOT phasing