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Crystal structure of the Bromo domain 1 in human Bromodomain Containing Protein 4 with a compound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6WGX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 0.2M NaNO3, 20% PEG3350, 10% Ethylene glycol, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.2 44.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.031 α = 90 b = 48.261 β = 90 c = 61.1 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 100 PIXEL DECTRIS EIGER X 9M 2024-09-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.92019 NSLS-II 17-ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 0.99 32.53 79.9 0.045 0.051 0.023 19.3 4.3 58095
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.992 1.009 6.4 0.44 0.622 0.44 1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE 0.99 32.53 1.36 55320 2849 76.09 0.1287 0.1276 0.1404 0.1497 0.1574
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.466 f_angle_d 1.171 f_chiral_restr 0.086 f_plane_restr 0.01 f_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1030 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms 42
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHENIX phasing