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CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX with compound SSR4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MXF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 277 20% w/v MMW PgSm, 100mM MES pH 6, 150 mM Ammonium nitrate, 5% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.12 42.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.36 α = 90 b = 44.13 β = 90 c = 77.79 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 2018-10-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9159 Diamond I04-1
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 1.2 77.79 95.7 0.999 21.7 5.1 39219
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 1.2 1.22 0.961
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE 3MXF 1.2 38.895 39155 1963 95.507 0.125 0.1235 0.1225 0.1485 0.1472 9.616
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] -0.398 0.655 -0.256
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.473 r_dihedral_angle_3_deg 10.762 r_dihedral_angle_4_deg 10.331 r_dihedral_angle_1_deg 6.061 r_lrange_it 2.945 r_lrange_other 2.939 r_scangle_it 1.715 r_scangle_other 1.714 r_angle_refined_deg 1.61 r_angle_other_deg 1.557
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.473 r_dihedral_angle_3_deg 10.762 r_dihedral_angle_4_deg 10.331 r_dihedral_angle_1_deg 6.061 r_lrange_it 2.945 r_lrange_other 2.939 r_scangle_it 1.715 r_scangle_other 1.714 r_angle_refined_deg 1.61 r_angle_other_deg 1.557 r_scbond_it 1.488 r_scbond_other 1.487 r_rigid_bond_restr 1.318 r_mcangle_other 1.176 r_mcangle_it 1.172 r_mcbond_it 0.873 r_mcbond_other 0.872 r_nbd_refined 0.231 r_nbtor_refined 0.19 r_nbd_other 0.188 r_symmetry_nbd_other 0.168 r_xyhbond_nbd_refined 0.151 r_symmetry_xyhbond_nbd_refined 0.123 r_symmetry_nbd_refined 0.11 r_chiral_restr 0.094 r_symmetry_nbtor_other 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1046 Nucleic Acid Atoms Solvent Atoms 215 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling REFMAC phasing