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Crystal structure of the first bromodomain of human BRD4 in complex with the ligand ZZ001229a
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Q3Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277.15 20% PEG6000 -- 10% ethylene glycol -- 0.1M HEPES pH 7.0 -- 0.2M sodium chloride
Crystal Properties Matthews coefficient Solvent content 2.09 41.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.239 α = 90.033 b = 44.093 β = 90 c = 78.479 γ = 90.026
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 XE 16M 2022-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9763 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.48 78.479 90.9 0.994 5.7 3.4 75591
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.48 1.506 51.3 0.394
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.48 78.479 75499 3632 90.769 0.185 0.1836 0.1836 0.2164 0.2168 14.278
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] 1.138 -0.234 -0.503 -0.571 -0.096 -0.567
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.294 r_dihedral_angle_3_deg 14.31 r_dihedral_angle_2_deg 6.601 r_lrange_it 5.569 r_dihedral_angle_1_deg 5.469 r_lrange_other 5.319 r_scangle_it 3.533 r_scangle_other 3.533 r_angle_refined_deg 2.905 r_scbond_it 2.254
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.294 r_dihedral_angle_3_deg 14.31 r_dihedral_angle_2_deg 6.601 r_lrange_it 5.569 r_dihedral_angle_1_deg 5.469 r_lrange_other 5.319 r_scangle_it 3.533 r_scangle_other 3.533 r_angle_refined_deg 2.905 r_scbond_it 2.254 r_scbond_other 2.254 r_mcangle_it 2.185 r_mcangle_other 2.185 r_mcbond_it 1.393 r_mcbond_other 1.386 r_angle_other_deg 0.474 r_symmetry_xyhbond_nbd_refined 0.27 r_symmetry_nbd_refined 0.234 r_nbd_refined 0.223 r_xyhbond_nbd_refined 0.204 r_nbd_other 0.194 r_symmetry_nbd_other 0.192 r_nbtor_refined 0.191 r_symmetry_xyhbond_nbd_other 0.088 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.075 r_ncsr_local_group_6 0.064 r_ncsr_local_group_2 0.062 r_ncsr_local_group_5 0.058 r_ncsr_local_group_3 0.057 r_ncsr_local_group_4 0.052 r_ncsr_local_group_1 0.049 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4224 Nucleic Acid Atoms Solvent Atoms 804 Heterogen Atoms 92
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling REFMAC phasing