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CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX with compound F1
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 8.5 277 0.1M bis-tris-propane pH 6.5, 20% PEG3350, 0.2M sodium fluoride, 10% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.15 42.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.73 α = 90 b = 43.99 β = 90 c = 78.06 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 2018-03-03 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 1.08 38.353 92.9 0.999 23.2 6 52386
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 1.08 1.1 0.981
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 1.08 38.352 52333 2621 92.585 0.124 0.1232 0.1213 0.1433 0.1423 9.386
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] 0.153 -0.98 0.827
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.939 r_dihedral_angle_3_deg 11.21 r_dihedral_angle_4_deg 8.994 r_dihedral_angle_1_deg 5.889 r_rigid_bond_restr 4.386 r_lrange_it 2.539 r_lrange_other 2.492 r_scangle_it 1.863 r_scangle_other 1.862 r_angle_refined_deg 1.725
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.939 r_dihedral_angle_3_deg 11.21 r_dihedral_angle_4_deg 8.994 r_dihedral_angle_1_deg 5.889 r_rigid_bond_restr 4.386 r_lrange_it 2.539 r_lrange_other 2.492 r_scangle_it 1.863 r_scangle_other 1.862 r_angle_refined_deg 1.725 r_scbond_it 1.696 r_scbond_other 1.694 r_angle_other_deg 1.593 r_mcangle_other 1.135 r_mcangle_it 1.134 r_mcbond_it 0.809 r_mcbond_other 0.801 r_nbd_other 0.228 r_nbd_refined 0.227 r_nbtor_refined 0.19 r_symmetry_nbd_refined 0.17 r_symmetry_nbd_other 0.161 r_symmetry_xyhbond_nbd_refined 0.145 r_xyhbond_nbd_refined 0.12 r_chiral_restr 0.104 r_symmetry_nbtor_other 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1049 Nucleic Acid Atoms Solvent Atoms 217 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling REFMAC phasing