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FIRST DOMAIN OF HUMAN BROMODOMAIN BRD4 IN COMPLEX WITH INHIBITOR #17
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OSS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 8.5 292 2.5mM of #17 inhibitor (in DMSO) final concentration.
Ratio 1:1 (protein:precipitant.
12mg/mL of BRD4(BD1) protein.
Precipitant agent: 0.3M NaNO3; 0.1M NaCl; 22% (w/v) PEG3350; 10% (w/v) ethylene glycol.
Cryoprotectant: 10 % (w/v) glycerol.
Crystal Properties Matthews coefficient Solvent content 2.04 39.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.284 α = 90 b = 47.498 β = 90 c = 58.468 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 PILATUS 6M 2016-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9 ESRF ID29
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 0.95 36.87 99.61 0.04761 0.05153 0.01942 0.999 16.41 6.8 78067 9.83
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 0.95 0.98 96.26 1.617 1.819 0.8059 0.434 0.78 4.7
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 2OSS 0.95 36.87 74651 3929 99.28 0.13641 0.1355 0.1435 0.15362 0.162 RANDOM 15.31
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] 0.24 -1.34 1.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.261 r_sphericity_free 26.476 r_dihedral_angle_4_deg 24.807 r_sphericity_bonded 15.939 r_dihedral_angle_3_deg 12.601 r_mcbond_other 10.281 r_mcbond_it 10.274 r_mcangle_it 8.821 r_mcangle_other 8.815 r_rigid_bond_restr 8.803
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.261 r_sphericity_free 26.476 r_dihedral_angle_4_deg 24.807 r_sphericity_bonded 15.939 r_dihedral_angle_3_deg 12.601 r_mcbond_other 10.281 r_mcbond_it 10.274 r_mcangle_it 8.821 r_mcangle_other 8.815 r_rigid_bond_restr 8.803 r_long_range_B_refined 7.169 r_long_range_B_other 7.167 r_scangle_other 6.845 r_dihedral_angle_1_deg 5.513 r_scbond_it 4.9 r_scbond_other 4.898 r_angle_refined_deg 2.363 r_angle_other_deg 1.697 r_chiral_restr 0.18 r_bond_refined_d 0.03 r_gen_planes_refined 0.014 r_bond_other_d 0.006 r_gen_planes_other 0.006 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1062 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling Coot model building PHASER phasing