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Crystal structure of human BRD4-BD1 bromodomain in complex with compound 960
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8B98
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291.15 Sodium Formate 5-6M, Glycerol 2-12%
Crystal Properties Matthews coefficient Solvent content 1.72 28.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.374 α = 90 b = 47.383 β = 90 c = 79.03 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 EIGER2 S 9M 2024-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.8731 ESRF ID30B
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 1.31 40.64 99.2 0.109 0.127 0.062 0.996 5.7 3.9 29805 12.32
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 1.31 1.332 1.31 1.529 0.771 0.444 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 MOLECULAR REPLACEMENT FREE R-VALUE 1.31 40.64 1.34 29761 1521 99.04 0.1475 0.1455 0.1463 0.187 0.1871 15.91
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 13.2806 f_angle_d 1.0294 f_chiral_restr 0.0699 f_plane_restr 0.0103 f_bond_d 0.0086
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1052 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms 50
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing autoPROC data processing